1
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Fenelon KD, Krause J, Koromila T. Opticool: Cutting-edge transgenic optical tools. PLoS Genet 2024; 20:e1011208. [PMID: 38517915 PMCID: PMC10959397 DOI: 10.1371/journal.pgen.1011208] [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] [Indexed: 03/24/2024] Open
Abstract
Only a few short decades have passed since the sequencing of GFP, yet the modern repertoire of transgenically encoded optical tools implies an exponential proliferation of ever improving constructions to interrogate the subcellular environment. A myriad of tags for labeling proteins, RNA, or DNA have arisen in the last few decades, facilitating unprecedented visualization of subcellular components and processes. Development of a broad array of modern genetically encoded sensors allows real-time, in vivo detection of molecule levels, pH, forces, enzyme activity, and other subcellular and extracellular phenomena in ever expanding contexts. Optogenetic, genetically encoded optically controlled manipulation systems have gained traction in the biological research community and facilitate single-cell, real-time modulation of protein function in vivo in ever broadening, novel applications. While this field continues to explosively expand, references are needed to assist scientists seeking to use and improve these transgenic devices in new and exciting ways to interrogate development and disease. In this review, we endeavor to highlight the state and trajectory of the field of in vivo transgenic optical tools.
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Affiliation(s)
- Kelli D. Fenelon
- Department of Biology, University of Texas at Arlington, Arlington, Texas, United States of America
| | - Julia Krause
- Department of Biology, University of Texas at Arlington, Arlington, Texas, United States of America
| | - Theodora Koromila
- Department of Biology, University of Texas at Arlington, Arlington, Texas, United States of America
- School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
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2
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Purohit K, Reddy N, Sunna A. Exploring the Potential of Bioactive Peptides: From Natural Sources to Therapeutics. Int J Mol Sci 2024; 25:1391. [PMID: 38338676 PMCID: PMC10855437 DOI: 10.3390/ijms25031391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 01/18/2024] [Accepted: 01/21/2024] [Indexed: 02/12/2024] Open
Abstract
Bioactive peptides, specific protein fragments with positive health effects, are gaining traction in drug development for advantages like enhanced penetration, low toxicity, and rapid clearance. This comprehensive review navigates the intricate landscape of peptide science, covering discovery to functional characterization. Beginning with a peptidomic exploration of natural sources, the review emphasizes the search for novel peptides. Extraction approaches, including enzymatic hydrolysis, microbial fermentation, and specialized methods for disulfide-linked peptides, are extensively covered. Mass spectrometric analysis techniques for data acquisition and identification, such as liquid chromatography, capillary electrophoresis, untargeted peptide analysis, and bioinformatics, are thoroughly outlined. The exploration of peptide bioactivity incorporates various methodologies, from in vitro assays to in silico techniques, including advanced approaches like phage display and cell-based assays. The review also discusses the structure-activity relationship in the context of antimicrobial peptides (AMPs), ACE-inhibitory peptides (ACEs), and antioxidative peptides (AOPs). Concluding with key findings and future research directions, this interdisciplinary review serves as a comprehensive reference, offering a holistic understanding of peptides and their potential therapeutic applications.
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Affiliation(s)
- Kruttika Purohit
- School of Natural Sciences, Macquarie University, Sydney, NSW 2109, Australia;
- Australian Research Council Industrial Transformation Training Centre for Facilitated Advancement of Australia’s Bioactives (FAAB), Sydney, NSW 2109, Australia;
| | - Narsimha Reddy
- Australian Research Council Industrial Transformation Training Centre for Facilitated Advancement of Australia’s Bioactives (FAAB), Sydney, NSW 2109, Australia;
- School of Science, Parramatta Campus, Western Sydney University, Penrith, NSW 2751, Australia
| | - Anwar Sunna
- School of Natural Sciences, Macquarie University, Sydney, NSW 2109, Australia;
- Australian Research Council Industrial Transformation Training Centre for Facilitated Advancement of Australia’s Bioactives (FAAB), Sydney, NSW 2109, Australia;
- Biomolecular Discovery Research Centre, Macquarie University, Sydney, NSW 2109, Australia
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3
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He S, Silva LD, Rutter GA, Lim GE. A high-throughput screening approach to discover potential colorectal cancer chemotherapeutics: Repurposing drugs to disrupt 14-3-3 protein-BAD interactions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.14.571727. [PMID: 38168191 PMCID: PMC10760183 DOI: 10.1101/2023.12.14.571727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Inducing apoptosis in different types of cancer cells is an effective therapeutic strategy. However, the success of existing chemotherapeutics can be compromised by tumor cell resistance and systemic off-target effects. Therefore, the discovery of pro-apoptotic compounds with minimal systemic side-effects is crucial. 14-3-3 proteins are molecular scaffolds that serve as important regulators of cell survival. Our previous study demonstrated that 14-3-3ζ can sequester BAD, a pro-apoptotic member of the BCL-2 protein family, in the cytoplasm and prevent its translocation to mitochondria to inhibit the induction of apoptosis. Despite being a critical mechanism of cell survival, it is unclear whether disrupting 14-3-3 protein:BAD interactions could be harnessed as a chemotherapeutic approach. Herein, we established a BRET-based high-throughput drug screening approach (Z'-score= 0.52) capable of identifying molecules that can disrupt 14-3-3ζ:BAD interactions. An FDA-approved drug library containing 1971 compounds was used for screening, and the capacity of identified hits to induce cell death was examined in NIH3T3-fibroblasts and colorectal cancer cell lines, HT-29 and Caco-2. Our in vitro results suggest that terfenadine, penfluridol, and lomitapide could be potentially repurposed for treating colorectal cancer. Moreover, our screening method demonstrates the feasibility of identifying pro-apoptotic agents that can be applied towards conditions where aberrant cell growth or function are key determinants of disease pathogenesis.
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Affiliation(s)
- Siyi He
- Department of Medicine, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
- Cardiometabolic axis, Centre de Recherche du Centre hospitalier de l’Université de Montréal (CRCHUM), Montréal, Québec, Canada
| | - Luis Delgadillo Silva
- Cardiometabolic axis, Centre de Recherche du Centre hospitalier de l’Université de Montréal (CRCHUM), Montréal, Québec, Canada
| | - Guy A. Rutter
- Department of Medicine, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
- Cardiometabolic axis, Centre de Recherche du Centre hospitalier de l’Université de Montréal (CRCHUM), Montréal, Québec, Canada
- Department of Diabetes, Endocrinology and Medicine, Faculty of Medicine, Imperial College, London, UK
- LKC School of Medicine, Nanyang Technological College, Singapore, Republic of Singapore
| | - Gareth E. Lim
- Department of Medicine, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
- Cardiometabolic axis, Centre de Recherche du Centre hospitalier de l’Université de Montréal (CRCHUM), Montréal, Québec, Canada
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4
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Sarhadi TR, Panse JS, Nagotu S. Mind the gap: Methods to study membrane contact sites. Exp Cell Res 2023; 431:113756. [PMID: 37633408 DOI: 10.1016/j.yexcr.2023.113756] [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: 03/28/2023] [Revised: 08/11/2023] [Accepted: 08/13/2023] [Indexed: 08/28/2023]
Abstract
Organelles are dynamic entities whose functions are essential for the optimum functioning of cells. It is now known that the juxtaposition of organellar membranes is essential for the exchange of metabolites and their communication. These functional apposition sites are termed membrane contact sites. Dynamic membrane contact sites between various sub-cellular structures such as mitochondria, endoplasmic reticulum, peroxisomes, Golgi apparatus, lysosomes, lipid droplets, plasma membrane, endosomes, etc. have been reported in various model systems. The burgeoning area of research on membrane contact sites has witnessed several manuscripts in recent years that identified the contact sites and components involved. Several methods have been developed to identify, measure and analyze the membrane contact sites. In this manuscript, we aim to discuss important methods developed to date that are used to study membrane contact sites.
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Affiliation(s)
- Tanveera Rounaque Sarhadi
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Janhavee Shirish Panse
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Shirisha Nagotu
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India.
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5
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Zhao L, Song Q, Mai W, Deng M, Lei Y, Chen L, Kong W, Zhang L, Zhang L, Li Y, Ye H, Qin Y, Zhang T, Hu Y, Ji T, Wei W. Engineering highly efficient NIR-II FRET platform for Background-Free homogeneous detection of SARS-CoV-2 neutralizing antibodies in whole blood. CHEMICAL ENGINEERING JOURNAL (LAUSANNE, SWITZERLAND : 1996) 2023; 468:143616. [PMID: 37251501 PMCID: PMC10195770 DOI: 10.1016/j.cej.2023.143616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 04/10/2023] [Accepted: 05/16/2023] [Indexed: 05/31/2023]
Abstract
Förster or fluorescence resonance energy transfer (FRET) enables to probe biomolecular interactions, thus playing a vital role in bioassays. However, conventional FRET platforms suffer from limited sensitivity due to the low FRET efficiency and poor anti-interference of existing FRET pairs. Here we report a NIR-II (1000-1700 nm) FRET platform with extremely high FRET efficiency and exceptional anti-interference capability. This NIR-II FRET platform is established based on a pair of lanthanides downshifting nanoparticles (DSNPs) by employing Nd3+ doped DSNPs as an energy donor and Yb3+ doped DSNPs as an energy acceptor. The maximum FRET efficiency of this well-engineered NIR-II FRET platform reaches up to 92.2%, which is much higher than most commonly used ones. Owing to the all-NIR advantage (λex = 808 nm, λem = 1064 nm), this highly efficient NIR-II FRET platform exhibits extraordinary anti-interference in whole blood, and thus enabling background-free homogeneous detection of SARS-CoV-2 neutralizing antibodies in clinical whole blood sample with high sensitivity (limit of detection = 0.5 μg/mL) and specificity. This work opens up new opportunities for realizing highly sensitive detection of various biomarkers in biological samples with severe background interference.
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Affiliation(s)
- Lei Zhao
- MOE & Guangdong Provincial Key Laboratory of Laser Life Science, Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, South China Normal University, Guangzhou, China
| | - Qingwei Song
- MOE & Guangdong Provincial Key Laboratory of Laser Life Science, Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, South China Normal University, Guangzhou, China
| | - Weikang Mai
- Clinical Laboratory Medicine Department, the Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Min Deng
- Clinical Laboratory Medicine Department, the Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yu Lei
- Clinical Laboratory Medicine Department, the Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Lu Chen
- Clinical Laboratory Medicine Department, the Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Weiya Kong
- Clinical Laboratory Medicine Department, the Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Lei Zhang
- Kidney Transplant Department, the Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Lin Zhang
- MOE & Guangdong Provincial Key Laboratory of Laser Life Science, Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, South China Normal University, Guangzhou, China
| | - Yantao Li
- MOE & Guangdong Provincial Key Laboratory of Laser Life Science, Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, South China Normal University, Guangzhou, China
| | - Huiru Ye
- MOE & Guangdong Provincial Key Laboratory of Laser Life Science, Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, South China Normal University, Guangzhou, China
| | - Yiru Qin
- Guangdong Provincial Key Laboratory of Occupational Disease Prevention and Treatment, Guangdong Province Hospital for Occupational Disease Prevention and Treatment, Guangzhou, China
| | - Tao Zhang
- MOE & Guangdong Provincial Key Laboratory of Laser Life Science, Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, South China Normal University, Guangzhou, China
| | - Yongjun Hu
- MOE & Guangdong Provincial Key Laboratory of Laser Life Science, Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, South China Normal University, Guangzhou, China
| | - Tianxing Ji
- Clinical Laboratory Medicine Department, the Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Wei Wei
- MOE & Guangdong Provincial Key Laboratory of Laser Life Science, Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, South China Normal University, Guangzhou, China
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6
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Abstract
The genetically encoded fluorescent sensors convert chemical and physical signals into light. They are powerful tools for the visualisation of physiological processes in living cells and freely moving animals. The fluorescent protein is the reporter module of a genetically encoded biosensor. In this study, we first review the history of the fluorescent protein in full emission spectra on a structural basis. Then, we discuss the design of the genetically encoded biosensor. Finally, we briefly review several major types of genetically encoded biosensors that are currently widely used based on their design and molecular targets, which may be useful for the future design of fluorescent biosensors.
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Affiliation(s)
- Minji Wang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, No. 3663 Zhong Shan Road North, Shanghai, 200062, China
| | - Yifan Da
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, No. 3663 Zhong Shan Road North, Shanghai, 200062, China
| | - Yang Tian
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, No. 3663 Zhong Shan Road North, Shanghai, 200062, China
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7
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He S, Lim GE. The Application of High-Throughput Approaches in Identifying Novel Therapeutic Targets and Agents to Treat Diabetes. Adv Biol (Weinh) 2023; 7:e2200151. [PMID: 36398493 DOI: 10.1002/adbi.202200151] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 10/04/2022] [Indexed: 11/19/2022]
Abstract
During the past decades, unprecedented progress in technologies has revolutionized traditional research methodologies. Among these, advances in high-throughput drug screening approaches have permitted the rapid identification of potential therapeutic agents from drug libraries that contain thousands or millions of molecules. Moreover, high-throughput-based therapeutic target discovery strategies can comprehensively interrogate relationships between biomolecules (e.g., gene, RNA, and protein) and diseases and significantly increase the authors' knowledge of disease mechanisms. Diabetes is a chronic disease primarily characterized by the incapacity of the body to maintain normoglycemia. The prevalence of diabetes in modern society has become a severe public health issue that threatens the well-being of millions of patients. Although a number of pharmacological treatments are available, there is no permanent cure for diabetes, and discovering novel therapeutic targets and agents continues to be an urgent need. The present review discusses the technical details of high-throughput screening approaches in drug discovery, followed by introducing the applications of such approaches to diabetes research. This review aims to provide an example of the applicability of high-throughput technologies in facilitating different aspects of disease research.
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Affiliation(s)
- Siyi He
- Department of Medicine, Université de Montréal, Pavillon Roger-Gaudry, 2900 Edouard Montpetit Blvd, Montreal, Québec, H3T 1J4, Canada.,Cardiometabolic Axis, Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), 900 rue St Denis, Montreal, Québec, H2X 0A9, Canada
| | - Gareth E Lim
- Department of Medicine, Université de Montréal, Pavillon Roger-Gaudry, 2900 Edouard Montpetit Blvd, Montreal, Québec, H3T 1J4, Canada.,Cardiometabolic Axis, Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), 900 rue St Denis, Montreal, Québec, H2X 0A9, Canada
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8
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Szewczyk MM, Owens DDG, Barsyte-Lovejoy D. Measuring Protein-Protein Interactions in Cells using Nanoluciferase Bioluminescence Resonance Energy Transfer (NanoBRET) Assay. Methods Mol Biol 2023; 2706:137-148. [PMID: 37558946 DOI: 10.1007/978-1-0716-3397-7_10] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/11/2023]
Abstract
Protein-protein interactions (PPIs) are increasingly recognized for their roles in functional cellular networks and their importance in disease-targeting contexts. Assessing PPI in the native cellular environment is challenging and requires specific and quantitative methods. Bioluminescence resonance energy transfer (BRET) is a biophysical process that can be used to quantify PPI. With Nanoluciferase bioluminescent protein as a donor and a fluorescent chloroalkane ligand covalently bound to HaloTag protein as an acceptor, NanoBRET provides a versatile and robust system to quantitatively measure PPI in living cells. BRET efficiency is proportional to the distance between the donor and acceptor, allowing for the measurement of PPI in real time. In this paper, we describe the use of NanoBRET to study specific interactions between proteins of interest in living cells that can be perturbed by using small-molecule antagonists and genetic mutations. Here, we provide a detailed protocol for expressing NanoLuc and HaloTag fusion proteins in cell culture and the necessary optimization of NanoBRET assay conditions. Our example results demonstrate the reliability and sensitivity of NanoBRET for measuring interactions between proteins, protein domains, and short peptides and quantitating the PPI antagonist compound activity in living cells.
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Affiliation(s)
| | - Dominic D G Owens
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada
| | - Dalia Barsyte-Lovejoy
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada.
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada.
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9
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Putt KS, Du Y, Fu H, Zhang ZY. High-throughput screening strategies for space-based radiation countermeasure discovery. LIFE SCIENCES IN SPACE RESEARCH 2022; 35:88-104. [PMID: 36336374 DOI: 10.1016/j.lssr.2022.07.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 06/13/2022] [Accepted: 07/19/2022] [Indexed: 06/16/2023]
Abstract
As humanity begins to venture further into space, approaches to better protect astronauts from the hazards found in space need to be developed. One particular hazard of concern is the complex radiation that is ever present in deep space. Currently, it is unlikely enough spacecraft shielding could be launched that would provide adequate protection to astronauts during long-duration missions such as a journey to Mars and back. In an effort to identify other means of protection, prophylactic radioprotective drugs have been proposed as a potential means to reduce the biological damage caused by this radiation. Unfortunately, few radioprotectors have been approved by the FDA for usage and for those that have been developed, they protect normal cells/tissues from acute, high levels of radiation exposure such as that from oncology radiation treatments. To date, essentially no radioprotectors have been developed that specifically counteract the effects of chronic low-dose rate space radiation. This review highlights how high-throughput screening (HTS) methodologies could be implemented to identify such a radioprotective agent. Several potential target, pathway, and phenotypic assays are discussed along with potential challenges towards screening for radioprotectors. Utilizing HTS strategies such as the ones proposed here have the potential to identify new chemical scaffolds that can be developed into efficacious radioprotectors that are specifically designed to protect astronauts during deep space journeys. The overarching goal of this review is to elicit broader interest in applying drug discovery techniques, specifically HTS towards the identification of radiation countermeasures designed to be efficacious towards the biological insults likely to be encountered by astronauts on long duration voyages.
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Affiliation(s)
- Karson S Putt
- Institute for Drug Discovery, Purdue University, West Lafayette IN 47907 USA
| | - Yuhong Du
- Department of Pharmacology and Chemical Biology and Emory Chemical Biology Discovery Center, Emory University School of Medicine, Atlanta, GA 30322 USA
| | - Haian Fu
- Department of Pharmacology and Chemical Biology and Emory Chemical Biology Discovery Center, Emory University School of Medicine, Atlanta, GA 30322 USA
| | - Zhong-Yin Zhang
- Institute for Drug Discovery, Purdue University, West Lafayette IN 47907 USA; Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette IN 47907 USA.
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10
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Ma Y, Luo M, Deng Y, Yang X, Wang X, Chen G, Qin Z, Deng Y, Nan M, Chen Y, Wang P, Wei H, Han L, Fang X, Liu Z. Antibiotic-Induced Primary Biles Inhibit SARS-CoV-2 Endoribonuclease Nsp15 Activity in Mouse Gut. Front Cell Infect Microbiol 2022; 12:896504. [PMID: 35967852 PMCID: PMC9366059 DOI: 10.3389/fcimb.2022.896504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 06/14/2022] [Indexed: 11/16/2022] Open
Abstract
The gut microbiome profile of COVID-19 patients was found to correlate with a viral load of SARS-CoV-2, COVID-19 severity, and dysfunctional immune responses, suggesting that gut microbiota may be involved in anti-infection. In order to investigate the role of gut microbiota in anti-infection against SARS-CoV-2, we established a high-throughput in vitro screening system for COVID-19 therapeutics by targeting the endoribonuclease (Nsp15). We also evaluated the activity inhibition of the target by substances of intestinal origin, using a mouse model in an attempt to explore the interactions between gut microbiota and SARS-CoV-2. The results unexpectedly revealed that antibiotic treatment induced the appearance of substances with Nsp15 activity inhibition in the intestine of mice. Comprehensive analysis based on functional profiling of the fecal metagenomes and endoribonuclease assay of antibiotic-enriched bacteria and metabolites demonstrated that the Nsp15 inhibitors were the primary bile acids that accumulated in the gut as a result of antibiotic-induced deficiency of bile acid metabolizing microbes. This study provides a new perspective on the development of COVID-19 therapeutics using primary bile acids.
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Affiliation(s)
- Yao Ma
- Department of Biotechnology, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Mei Luo
- Department of Biotechnology, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Yusheng Deng
- Department of Scientific Research, KMHD, Shenzhen, China
| | - Xiaoman Yang
- Department of Biotechnology, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Xionglue Wang
- Department of Biotechnology, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Guozhong Chen
- Department of Biotechnology, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Zixin Qin
- Department of Biotechnology, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Yun Deng
- Department of Biotechnology, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Meiling Nan
- Key Laboratory for Experimental Teratology of Ministry of Education and Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Yang Chen
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Peihui Wang
- Key Laboratory for Experimental Teratology of Ministry of Education and Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Hong Wei
- State Key Laboratory of Agricultural Microbiology, College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, China
| | - Lijuan Han
- Department of Scientific Research, KMHD, Shenzhen, China
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
- *Correspondence: Zhi Liu, ; Xiaodong Fang, ; Lijuan Han,
| | - Xiaodong Fang
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
- *Correspondence: Zhi Liu, ; Xiaodong Fang, ; Lijuan Han,
| | - Zhi Liu
- Department of Biotechnology, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
- *Correspondence: Zhi Liu, ; Xiaodong Fang, ; Lijuan Han,
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11
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Vu V, Szewczyk MM, Nie DY, Arrowsmith CH, Barsyte-Lovejoy D. Validating Small Molecule Chemical Probes for Biological Discovery. Annu Rev Biochem 2022; 91:61-87. [PMID: 35363509 DOI: 10.1146/annurev-biochem-032620-105344] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Small molecule chemical probes are valuable tools for interrogating protein biological functions and relevance as a therapeutic target. Rigorous validation of chemical probe parameters such as cellular potency and selectivity is critical to unequivocally linking biological and phenotypic data resulting from treatment with a chemical probe to the function of a specific target protein. A variety of modern technologies are available to evaluate cellular potency and selectivity, target engagement, and functional response biomarkers of chemical probe compounds. Here, we review these technologies and the rationales behind using them for the characterization and validation of chemical probes. In addition, large-scale phenotypic characterization of chemical probes through chemical genetic screening is increasingly leading to a wealth of information on the cellular pharmacology and disease involvement of potential therapeutic targets. Extensive compound validation approaches and integration of phenotypic information will lay foundations for further use of chemical probes in biological discovery. Expected final online publication date for the Annual Review of Biochemistry, Volume 91 is June 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Victoria Vu
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada; .,Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Magdalena M Szewczyk
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada;
| | - David Y Nie
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada; .,Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Cheryl H Arrowsmith
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada; .,Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Dalia Barsyte-Lovejoy
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada; .,Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada
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12
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Johnson CW, Seo HS, Terrell EM, Yang MH, KleinJan F, Gebregiworgis T, Gasmi-Seabrook GMC, Geffken EA, Lakhani J, Song K, Bashyal P, Popow O, Paulo JA, Liu A, Mattos C, Marshall CB, Ikura M, Morrison DK, Dhe-Paganon S, Haigis KM. Regulation of GTPase function by autophosphorylation. Mol Cell 2022; 82:950-968.e14. [PMID: 35202574 PMCID: PMC8986090 DOI: 10.1016/j.molcel.2022.02.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 11/29/2021] [Accepted: 02/04/2022] [Indexed: 10/19/2022]
Abstract
A unifying feature of the RAS superfamily is a conserved GTPase cycle by which these proteins transition between active and inactive states. We demonstrate that autophosphorylation of some GTPases is an intrinsic regulatory mechanism that reduces nucleotide hydrolysis and enhances nucleotide exchange, altering the on/off switch that forms the basis for their signaling functions. Using X-ray crystallography, nuclear magnetic resonance spectroscopy, binding assays, and molecular dynamics on autophosphorylated mutants of H-RAS and K-RAS, we show that phosphoryl transfer from GTP requires dynamic movement of the switch II region and that autophosphorylation promotes nucleotide exchange by opening the active site and extracting the stabilizing Mg2+. Finally, we demonstrate that autophosphorylated K-RAS exhibits altered effector interactions, including a reduced affinity for RAF proteins in mammalian cells. Thus, autophosphorylation leads to altered active site dynamics and effector interaction properties, creating a pool of GTPases that are functionally distinct from their non-phosphorylated counterparts.
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Affiliation(s)
- Christian W Johnson
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Hyuk-Soo Seo
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Elizabeth M Terrell
- Laboratory of Cell and Developmental Signaling, NCI-Frederick, Frederick, MD 21702, USA
| | - Moon-Hee Yang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Fenneke KleinJan
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Teklab Gebregiworgis
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | | | - Ezekiel A Geffken
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Jimit Lakhani
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Kijun Song
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Puspalata Bashyal
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Olesja Popow
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Andrea Liu
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Carla Mattos
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | | | - Mitsuhiko Ikura
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Deborah K Morrison
- Laboratory of Cell and Developmental Signaling, NCI-Frederick, Frederick, MD 21702, USA
| | - Sirano Dhe-Paganon
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Kevin M Haigis
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.
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13
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A Real-Time, Plate-Based BRET Assay for Detection of cGMP in Primary Cells. Int J Mol Sci 2022; 23:ijms23031908. [PMID: 35163827 PMCID: PMC8837005 DOI: 10.3390/ijms23031908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/30/2022] [Accepted: 02/04/2022] [Indexed: 11/30/2022] Open
Abstract
Cyclic guanosine monophosphate (cGMP) is a second messenger involved in the regulation of numerous physiological processes. The modulation of cGMP is important in many diseases, but reliably assaying cGMP in live cells in a plate-based format with temporal resolution is challenging. The Förster/fluorescence resonance energy transfer (FRET)-based biosensor cGES-DE5 has a high temporal resolution and high selectivity for cGMP over cAMP, so we converted it to use bioluminescence resonance energy transfer (BRET), which is more compatible with plate-based assays. This BRET variant, called CYGYEL (cyclic GMP sensor using YFP-PDE5-Rluc8), was cloned into a lentiviral vector for use across different mammalian cell types. CYGYEL was characterised in HEK293T cells using the nitric oxide donor diethylamine NONOate (DEA), where it was shown to be dynamic, reversible, and able to detect cGMP with or without the use of phosphodiesterase inhibitors. In human primary vascular endothelial and smooth muscle cells, CYGYEL successfully detected cGMP mediated through either soluble or particulate guanylate cyclase using DEA or C-type natriuretic peptide, respectively. Notably, CYGYEL detected differences in kinetics and strength of signal both between ligands and between cell types. CYGYEL remained selective for cGMP over cAMP, but this selectivity was reduced compared to cGES-DE5. CYGYEL streamlines the process of cGMP detection in plate-based assays and can be used to detect cGMP activity across a range of cell types.
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14
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Fernández LR, Mild J, Edreira MM. Screening of Protein-Protein Interaction Modulators Using BRET-Based Technology. Methods Mol Biol 2022; 2525:173-183. [PMID: 35836067 DOI: 10.1007/978-1-0716-2473-9_12] [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: 06/15/2023]
Abstract
Protein-protein interactions (PPIs) play central roles in most molecular mechanisms underlying cellular and biological processes. Within the methods developed to study PPIs is bioluminescence resonance energy transfer (BRET). Taking advantage of this technique, we have set a BRET-based assay that enables the screening of modulators of essential PPIs for Trypanosoma cruzi survival. Considering the complexity of the evaluated mixture, pure chemical compounds or natural extracts, two approaches are described, BRET in living cells or from lysates.
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Affiliation(s)
- Lucia R Fernández
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Orgánica, Buenos Aires, Argentina
- CONICET-Universidad de Buenos Aires, Unidad de Microanálisis y Métodos Físicos Aplicados a la Química Orgánica (UMYMFOR), Buenos Aires, Argentina
| | - Jesica Mild
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Buenos Aires, Argentina
- CONICET-Universidad de Buenos Aires, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Buenos Aires, Argentina
| | - Martin M Edreira
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Buenos Aires, Argentina.
- CONICET-Universidad de Buenos Aires, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Buenos Aires, Argentina.
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA.
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15
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Azad T, Janse van Rensburg HJ, Morgan J, Rezaei R, Crupi MJF, Chen R, Ghahremani M, Jamalkhah M, Forbes N, Ilkow C, Bell JC. Luciferase-Based Biosensors in the Era of the COVID-19 Pandemic. ACS NANOSCIENCE AU 2021; 1:15-37. [PMID: 37579261 PMCID: PMC8370122 DOI: 10.1021/acsnanoscienceau.1c00009] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Luciferase-based biosensors have a wide range of applications and assay formats, including their relatively recent use in the study of viruses. Split luciferase, bioluminescence resonance energy transfer, circularly permuted luciferase, cyclic luciferase, and dual luciferase systems have all been used to interrogate the structure and function of prominent viruses infecting humans, animals, and plants. The utility of these assays is demonstrated by numerous studies which have not only successfully characterized interactions between viral and host cell proteins but that have also used these systems to identify viral inhibitors. In the present COVID-19 pandemic, luciferase-based biosensors are already playing a critical role in the study of the culprit virus SARS-CoV-2 as well as in the development of serological assays and drug development via high-throughput screening. In this review paper, we provide a summary of existing luciferase-based biosensors and their applications in virology.
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Affiliation(s)
- Taha Azad
- Centre
for Innovative Cancer Research, Ottawa Hospital
Research Institute, Ottawa K1H 8L6, Canada
- Department
of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa K1H 8M5, Canada
| | | | - Jessica Morgan
- Centre
for Innovative Cancer Research, Ottawa Hospital
Research Institute, Ottawa K1H 8L6, Canada
- Department
of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa K1H 8M5, Canada
| | - Reza Rezaei
- Centre
for Innovative Cancer Research, Ottawa Hospital
Research Institute, Ottawa K1H 8L6, Canada
- Department
of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa K1H 8M5, Canada
| | - Mathieu J. F. Crupi
- Centre
for Innovative Cancer Research, Ottawa Hospital
Research Institute, Ottawa K1H 8L6, Canada
- Department
of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa K1H 8M5, Canada
| | - Rui Chen
- Centre
for Innovative Cancer Research, Ottawa Hospital
Research Institute, Ottawa K1H 8L6, Canada
- Department
of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa K1H 8M5, Canada
| | - Mina Ghahremani
- Canada
Department of Biology, University of Ottawa, Ottawa K1N 6N5, Canada
| | - Monire Jamalkhah
- Centre
for Innovative Cancer Research, Ottawa Hospital
Research Institute, Ottawa K1H 8L6, Canada
- Department
of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa K1H 8M5, Canada
| | - Nicole Forbes
- Centre
for Communicable Diseases and Infection Control, Public Health Agency of Canada, Ottawa K2E 1B6, Canada
| | - Carolina Ilkow
- Centre
for Innovative Cancer Research, Ottawa Hospital
Research Institute, Ottawa K1H 8L6, Canada
- Department
of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa K1H 8M5, Canada
| | - John C. Bell
- Centre
for Innovative Cancer Research, Ottawa Hospital
Research Institute, Ottawa K1H 8L6, Canada
- Department
of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa K1H 8M5, Canada
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16
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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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17
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Engineering with NanoLuc: a playground for the development of bioluminescent protein switches and sensors. Biochem Soc Trans 2021; 48:2643-2655. [PMID: 33242085 DOI: 10.1042/bst20200440] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 10/21/2020] [Accepted: 10/26/2020] [Indexed: 12/11/2022]
Abstract
The small engineered luciferase NanoLuc has rapidly become a powerful tool in the fields of biochemistry, chemical biology, and cell biology due to its exceptional brightness and stability. The continuously expanding NanoLuc toolbox has been employed in applications ranging from biosensors to molecular and cellular imaging, and currently includes split complementation variants, engineering techniques for spectral tuning, and bioluminescence resonance energy transfer-based concepts. In this review, we provide an overview of state-of-the-art NanoLuc-based sensors and switches with a focus on the underlying protein engineering approaches. We discuss the advantages and disadvantages of various strategies with respect to sensor sensitivity, modularity, and dynamic range of the sensor and provide a perspective on future strategies and applications.
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18
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Abstract
Nanobodies have emerged as useful tools to study G protein-coupled receptor (GPCR) structure, dynamic, and subcellular localization. Initially, several nanobodies have been developed as chaperones to facilitate GPCR crystallization. To explore their potential as biosensors to monitor receptor activation and dynamics, we here described protocols to characterize nanobody's interaction with GPCRs and their application as probes for protein identification and visualization on the cellular level. We also introduced a chimeric approach to enable a kappa-opioid receptor derived nanobody to bind to other GPCRs, including orphan GPCRs whose endogenous ligand or intracellular transducers are unknown. This approach provides a reporter assay to identify tool molecules to study the function of orphan GPCRs.
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Affiliation(s)
- Amal El Daibani
- Department of Anesthesiology, Washington University School of Medicine, St. Louis, MO, United States
| | - Tao Che
- Department of Anesthesiology, Washington University School of Medicine, St. Louis, MO, United States; Center for Clinical Pharmacology, University of Health Sciences and Pharmacy in St. Louis and Washington University School of Medicine, St. Louis, MO, United States.
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19
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Wang Z, Xia H, Chen B, Wang Y, Yin Q, Yan Y, Yang Y, Tang M, Liu J, Zhao R, Li W, Zhang Q, Wang Y. pH‐Amplified CRET Nanoparticles for In Vivo Imaging of Tumor Metastatic Lymph Nodes. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202102044] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Zenghui Wang
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University Beijing 100191 China
- Beijing Key Laboratory of Molecular Pharmaceutics School of Pharmaceutical Sciences Peking University Beijing 100191 China
| | - Heming Xia
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University Beijing 100191 China
- Beijing Key Laboratory of Molecular Pharmaceutics School of Pharmaceutical Sciences Peking University Beijing 100191 China
| | - Binlong Chen
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University Beijing 100191 China
- Beijing Key Laboratory of Molecular Pharmaceutics School of Pharmaceutical Sciences Peking University Beijing 100191 China
| | - Yaoqi Wang
- Beijing Key Laboratory of Molecular Pharmaceutics School of Pharmaceutical Sciences Peking University Beijing 100191 China
| | - Qingqing Yin
- Beijing Key Laboratory of Molecular Pharmaceutics School of Pharmaceutical Sciences Peking University Beijing 100191 China
| | - Yue Yan
- Beijing Key Laboratory of Molecular Pharmaceutics School of Pharmaceutical Sciences Peking University Beijing 100191 China
| | - Ye Yang
- Beijing Key Laboratory of Molecular Pharmaceutics School of Pharmaceutical Sciences Peking University Beijing 100191 China
| | - Mingmei Tang
- Beijing Key Laboratory of Molecular Pharmaceutics School of Pharmaceutical Sciences Peking University Beijing 100191 China
| | - Jianxiong Liu
- Beijing Key Laboratory of Molecular Pharmaceutics School of Pharmaceutical Sciences Peking University Beijing 100191 China
| | - Ruiyang Zhao
- Beijing Key Laboratory of Molecular Pharmaceutics School of Pharmaceutical Sciences Peking University Beijing 100191 China
| | - Wenzhe Li
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University Beijing 100191 China
| | - Qiang Zhang
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University Beijing 100191 China
- Beijing Key Laboratory of Molecular Pharmaceutics School of Pharmaceutical Sciences Peking University Beijing 100191 China
| | - Yiguang Wang
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University Beijing 100191 China
- Beijing Key Laboratory of Molecular Pharmaceutics School of Pharmaceutical Sciences Peking University Beijing 100191 China
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20
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pH‐Amplified CRET Nanoparticles for In Vivo Imaging of Tumor Metastatic Lymph Nodes. Angew Chem Int Ed Engl 2021; 60:14512-14520. [DOI: 10.1002/anie.202102044] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 04/08/2021] [Indexed: 12/12/2022]
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21
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Evolution of biophysical tools for quantitative protein interactions and drug discovery. Emerg Top Life Sci 2021; 5:1-12. [PMID: 33739398 DOI: 10.1042/etls20200258] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 02/23/2021] [Accepted: 02/25/2021] [Indexed: 12/13/2022]
Abstract
With millions of signalling events occurring simultaneously, cells process a continuous flux of information. The genesis, processing, and regulation of information are dictated by a huge network of protein interactions. This is proven by the fact that alterations in the levels of proteins, single amino acid changes, post-translational modifications, protein products arising out of gene fusions alter the interaction landscape leading to diseases such as congenital disorders, deleterious syndromes like cancer, and crippling diseases like the neurodegenerative disorders which are often fatal. Needless to say, there is an immense effort to understand the biophysical basis of such direct interactions between any two proteins, the structure, domains, and sequence motifs involved in tethering them, their spatio-temporal regulation in cells, the structure of the network, and their eventual manipulation for intervention in diseases. In this chapter, we will deliberate on a few techniques that allow us to dissect the thermodynamic and kinetic aspects of protein interaction, how innovation has rendered some of the traditional techniques applicable for rapid analysis of multiple samples using small amounts of material. These advances coupled with automation are catching up with the genome-wide or proteome-wide studies aimed at identifying new therapeutic targets. The chapter will also summarize how some of these techniques are suited either in the standalone mode or in combination with other biophysical techniques for the drug discovery process.
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22
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Pipchuk A, Yang X. Using Biosensors to Study Protein-Protein Interaction in the Hippo Pathway. Front Cell Dev Biol 2021; 9:660137. [PMID: 33981705 PMCID: PMC8107278 DOI: 10.3389/fcell.2021.660137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 04/06/2021] [Indexed: 11/18/2022] Open
Abstract
The Hippo signaling network is dependent on protein–protein interactions (PPIs) as a mechanism of signal transduction to regulate organ size, cellular proliferation and differentiation, tumorigenesis, and other cellular processes. Current efforts aim to resolve the complex regulation of upstream Hippo components or focus on identifying targeted drugs for use in cancer therapy. Despite extensive characterization of the Hippo pathway interactome by affinity purification mass spectrometry (AP-MS) and other methodologies, previous research methods have not been sufficient to achieve these aims. In this review, we describe several recent studies that make use of luciferase-based biosensors as a new approach to study the Hippo Pathway. These biosensors serve as powerful tools with which to study PPIs both in vitro using purified biosensor proteins, and in real time in live cells. Notably, luciferase biosensors have excellent sensitivity and have been used to screen for upstream kinase regulators of the Hippo pathway. Furthermore, the high sensitivity and stability of these biosensors enables their application in high throughput screening for Hippo-targeted chemotherapeutics. Finally, we describe the strengths and weaknesses of this method relative to AP-MS and discuss potential future directions for using biosensors to study Hippo signaling.
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Affiliation(s)
- Alexander Pipchuk
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, ON, Canada
| | - Xiaolong Yang
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, ON, Canada
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23
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Modeling Pharmacokinetics and Pharmacodynamics of Therapeutic Antibodies: Progress, Challenges, and Future Directions. Pharmaceutics 2021; 13:pharmaceutics13030422. [PMID: 33800976 PMCID: PMC8003994 DOI: 10.3390/pharmaceutics13030422] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 03/18/2021] [Accepted: 03/18/2021] [Indexed: 12/29/2022] Open
Abstract
With more than 90 approved drugs by 2020, therapeutic antibodies have played a central role in shifting the treatment landscape of many diseases, including autoimmune disorders and cancers. While showing many therapeutic advantages such as long half-life and highly selective actions, therapeutic antibodies still face many outstanding issues associated with their pharmacokinetics (PK) and pharmacodynamics (PD), including high variabilities, low tissue distributions, poorly-defined PK/PD characteristics for novel antibody formats, and high rates of treatment resistance. We have witnessed many successful cases applying PK/PD modeling to answer critical questions in therapeutic antibodies’ development and regulations. These models have yielded substantial insights into antibody PK/PD properties. This review summarized the progress, challenges, and future directions in modeling antibody PK/PD and highlighted the potential of applying mechanistic models addressing the development questions.
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24
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Functional Imaging Using Bioluminescent Reporter Genes in Living Subjects. Mol Imaging 2021. [DOI: 10.1016/b978-0-12-816386-3.00004-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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25
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Schihada H, Nemec K, Lohse MJ, Maiellaro I. Bioluminescence in G Protein-Coupled Receptors Drug Screening Using Nanoluciferase and Halo-Tag Technology. Methods Mol Biol 2021; 2268:137-147. [PMID: 34085266 DOI: 10.1007/978-1-0716-1221-7_9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Here we describe the stepwise application of bioluminescence resonance energy transfer (BRET)-based conformational receptor biosensors to study GPCR activation in intact cells. This technology can be easily adopted to various plate reader devices and microtiter plate formats. Due to the high sensitivity of these BRET-based receptor biosensors and their ability to quantify simultaneously receptor activation/de-activation kinetics as well as compound efficacy and potency, these optical tools provide the most direct and unbiased approach to monitor GPCR activity in a high-throughput-compatible assay format, representing a novel promising tool for the discovery of potential GPCR therapeutics.
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Affiliation(s)
- Hannes Schihada
- Section of Receptor Biology & Signaling, Department of Physiology & Pharmacology, Karolinska Institutet, Stockholm, Sweden.,Institute of Pharmacology and Toxicology, University of Wuerzburg, Wuerzburg, Germany
| | - Katarina Nemec
- Max-Delbrueck-Center for Molecular Medicine, Berlin, Germany
| | - Martin J Lohse
- Institute of Pharmacology and Toxicology, University of Wuerzburg, Wuerzburg, Germany.,Max-Delbrueck-Center for Molecular Medicine, Berlin, Germany.,ISAR Bioscience, Planegg, Germany
| | - Isabella Maiellaro
- School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham, UK.
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26
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Liu TY. Using Tripartite Split-sfGFP for the Study of Membrane Protein-Protein Interactions. Methods Mol Biol 2021; 2200:323-336. [PMID: 33175385 DOI: 10.1007/978-1-0716-0880-7_15] [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: 12/23/2022]
Abstract
The study of protein-protein interaction (PPI) is critical for understanding cellular processes within biological systems. The conventional biomolecular fluorescence complementation (BiFC) or bipartite split-fluorescent protein (FP) is a noninvasive fluorescent-based technique that enables direct visualization of PPI in living cells once the two nonfluorescent fragments are brought into close vicinity. However, BiFC can potentially lead to a high background noise arising from an inherent feature of the irreversible self-assembly of the nonfluorescent fragments. Recently, the newly developed tripartite split-sfGFP method was demonstrated to detect membrane PPIs in plant cells without spurious background signals even when fusion proteins are highly expressed and accessible to the compartments of interaction. Here we describe a protocol for using the ß-Estradiol-inducible tripartite split-sfGFP assay for side-by-side analyses of in vivo PPI along with in situ subcellular localization of fusion proteins in agroinfiltrated Nicotiana benthamiana leaves.
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Affiliation(s)
- Tzu-Yin Liu
- Department of Life Science and Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan.
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27
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Karakostis K, López I, Peña-Balderas AM, Fåhareus R, Olivares-Illana V. Molecular and Biochemical Techniques for Deciphering p53-MDM2 Regulatory Mechanisms. Biomolecules 2020; 11:36. [PMID: 33396576 PMCID: PMC7824699 DOI: 10.3390/biom11010036] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 12/12/2020] [Accepted: 12/14/2020] [Indexed: 12/12/2022] Open
Abstract
The p53 and Mouse double minute 2 (MDM2) proteins are hubs in extensive networks of interactions with multiple partners and functions. Intrinsically disordered regions help to adopt function-specific structural conformations in response to ligand binding and post-translational modifications. Different techniques have been used to dissect interactions of the p53-MDM2 pathway, in vitro, in vivo, and in situ each having its own advantages and disadvantages. This review uses the p53-MDM2 to show how different techniques can be employed, illustrating how a combination of in vitro and in vivo techniques is highly recommended to study the spatio-temporal location and dynamics of interactions, and to address their regulation mechanisms and functions. By using well-established techniques in combination with more recent advances, it is possible to rapidly decipher complex mechanisms, such as the p53 regulatory pathway, and to demonstrate how protein and nucleotide ligands in combination with post-translational modifications, result in inter-allosteric and intra-allosteric interactions that govern the activity of the protein complexes and their specific roles in oncogenesis. This promotes elegant therapeutic strategies that exploit protein dynamics to target specific interactions.
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Affiliation(s)
- Konstantinos Karakostis
- Inserm UMRS1131, Institut de Génétique Moléculaire, Université Paris 7, Hôpital St. Louis, F-75010 Paris, France; (K.K.); (R.F.)
| | - Ignacio López
- Biochemistry-Molecular Biology, Faculty of Science, Universidad de la República, Iguá 4225, Montevideo 11400, Uruguay;
| | - Ana M. Peña-Balderas
- Laboratorio de Interacciones Biomoleculares y Cáncer, Instituto de Física Universidad Autónoma de San Luis Potosí, Manuel Nava 6, Zona Universitaria, San Luis Potosí 78290, Mexico;
| | - Robin Fåhareus
- Inserm UMRS1131, Institut de Génétique Moléculaire, Université Paris 7, Hôpital St. Louis, F-75010 Paris, France; (K.K.); (R.F.)
- Regional Centre for Applied Molecular Oncology (RECAMO), Masaryk Memorial Cancer Institute, Zluty Kopec 7, 65653 Brno, Czech Republic
- Department of Medical Biosciences, Building 6M, Umeå University, 90185 Umeå, Sweden
- International Center for Cancer Vaccine Science (ICCVS), University of Gdańsk, Science, ul. Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Vanesa Olivares-Illana
- Laboratorio de Interacciones Biomoleculares y Cáncer, Instituto de Física Universidad Autónoma de San Luis Potosí, Manuel Nava 6, Zona Universitaria, San Luis Potosí 78290, Mexico;
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Zhao T, Masuda T, Miyoshi E, Takai M. High Dye-Loaded and Thin-Shell Fluorescent Polymeric Nanoparticles for Enhanced FRET Imaging of Protein-Specific Sialylation on the Cell Surface. Anal Chem 2020; 92:13271-13280. [DOI: 10.1021/acs.analchem.0c02502] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Tingbi Zhao
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan
| | - Tsukuru Masuda
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan
| | - Eiji Miyoshi
- Department of Molecular Biochemistry and Clinical Investigation, School of Medicine, Osaka University, Osaka 565-0871, Japan
| | - Madoka Takai
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan
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29
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Blay V, Tolani B, Ho SP, Arkin MR. High-Throughput Screening: today's biochemical and cell-based approaches. Drug Discov Today 2020; 25:1807-1821. [PMID: 32801051 DOI: 10.1016/j.drudis.2020.07.024] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 07/01/2020] [Accepted: 07/30/2020] [Indexed: 12/13/2022]
Abstract
High-throughput screening (HTS) provides starting chemical matter in the adventure of developing a new drug. In this review, we survey several HTS methods used today for hit identification, organized in two main flavors: biochemical and cell-based assays. Biochemical assays discussed include fluorescence polarization and anisotropy, FRET, TR-FRET, and fluorescence lifetime analysis. Binding-based methods are also surveyed, including NMR, SPR, mass spectrometry, and DSF. On the other hand, cell-based assays discussed include viability, reporter gene, second messenger, and high-throughput microscopy assays. We devote some emphasis to high-content screening, which is becoming very popular. An advisable stage after hit discovery using phenotypic screens is target deconvolution, and we provide an overview of current chemical proteomics, in silico, and chemical genetics tools. Emphasis is made on recent CRISPR/dCas-based screens. Lastly, we illustrate some of the considerations that inform the choice of HTS methods and point to some areas with potential interest for future research.
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Affiliation(s)
- Vincent Blay
- Division of Biomaterials and Bioengineering, School of Dentistry, University of California San Francisco, San Francisco, CA 94143, USA; Department of Urology, School of Medicine, University of California San Francisco, San Francisco, CA 94143, USA.
| | - Bhairavi Tolani
- Thoracic Oncology Program, Department of Surgery, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Sunita P Ho
- Division of Biomaterials and Bioengineering, School of Dentistry, University of California San Francisco, San Francisco, CA 94143, USA; Department of Urology, School of Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - Michelle R Arkin
- Department of Pharmaceutical Chemistry and the Small Molecule Discovery Center, University of California, San Francisco, CA, USA.
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30
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Bouquier N, Moutin E, Tintignac LA, Reverbel A, Jublanc E, Sinnreich M, Chastagnier Y, Averous J, Fafournoux P, Verpelli C, Boeckers T, Carnac G, Perroy J, Ollendorff V. AIMTOR, a BRET biosensor for live imaging, reveals subcellular mTOR signaling and dysfunctions. BMC Biol 2020; 18:81. [PMID: 32620110 PMCID: PMC7334845 DOI: 10.1186/s12915-020-00790-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 05/06/2020] [Indexed: 11/24/2022] Open
Abstract
Background mTOR signaling is an essential nutrient and energetic sensing pathway. Here we describe AIMTOR, a sensitive genetically encoded BRET (Bioluminescent Resonance Energy Transfer) biosensor to study mTOR activity in living cells. Results As a proof of principle, we show in both cell lines and primary cell cultures that AIMTOR BRET intensities are modified by mTOR activity changes induced by specific inhibitors and activators of mTORC1 including amino acids and insulin. We further engineered several versions of AIMTOR enabling subcellular-specific assessment of mTOR activities. We then used AIMTOR to decipher mTOR signaling in physio-pathological conditions. First, we show that mTORC1 activity increases during muscle cell differentiation and in response to leucine stimulation in different subcellular compartments such as the cytosol and at the surface of the lysosome, the nucleus, and near the mitochondria. Second, in hippocampal neurons, we found that the enhancement of neuronal activity increases mTOR signaling. AIMTOR further reveals mTOR-signaling dysfunctions in neurons from mouse models of autism spectrum disorder. Conclusions Altogether, our results demonstrate that AIMTOR is a sensitive and specific tool to investigate mTOR-signaling dynamics in living cells and phenotype mTORopathies.
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Affiliation(s)
| | - Enora Moutin
- IGF, University of Montpellier, CNRS, INSERM, Montpellier, France
| | - Lionel A Tintignac
- University Hospital Basel, Department of Biomedecine, Basel, Switzerland
| | | | - Elodie Jublanc
- DMEM, University of Montpellier, INRAE, Montpellier, France
| | - Michael Sinnreich
- University Hospital Basel, Department of Biomedecine, Basel, Switzerland
| | - Yan Chastagnier
- IGF, University of Montpellier, CNRS, INSERM, Montpellier, France
| | - Julien Averous
- Université Clermont Auvergne, INRAE, Unité de Nutrition Humaine, UMR1019, Clermont-Ferrand, France
| | - Pierre Fafournoux
- Université Clermont Auvergne, INRAE, Unité de Nutrition Humaine, UMR1019, Clermont-Ferrand, France
| | - Chiara Verpelli
- Cnr Institute of Neuroscience, Via Vanvitelli, 3220129, Milan, Italy
| | - Tobias Boeckers
- Anatomie und Zellbiologie Universität Ulm, Albert-Einstein Allee 11, Raumnummer 4105, M24, 89081, Ulm, Germany
| | - Gilles Carnac
- Phymedexp, University of Montpellier, CNRS, INSERM, Montpellier, France
| | - Julie Perroy
- IGF, University of Montpellier, CNRS, INSERM, Montpellier, France.
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31
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Wang L, Saarela J, Poque S, Valkonen JP. Development of FRET-based high-throughput screening for viral RNase III inhibitors. MOLECULAR PLANT PATHOLOGY 2020; 21:961-974. [PMID: 32436305 PMCID: PMC7280029 DOI: 10.1111/mpp.12942] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 03/09/2020] [Accepted: 03/16/2020] [Indexed: 06/11/2023]
Abstract
The class 1 ribonuclease III (RNase III) encoded by Sweet potato chlorotic stunt virus (CSR3) suppresses RNA silencing in plant cells and thereby counters the host antiviral response by cleaving host small interfering RNAs, which are indispensable components of the plant RNA interference (RNAi) pathway. The synergy between sweet potato chlorotic stunt virus and sweet potato feathery mottle virus can reduce crop yields by 90%. Inhibitors of CSR3 might prove efficacious to counter this viral threat, yet no screen has been carried out to identify such inhibitors. Here, we report a novel high-throughput screening (HTS) assay based on fluorescence resonance energy transfer (FRET) for identifying inhibitors of CSR3. For monitoring CSR3 activity via HTS, we used a small interfering RNA substrate that was labelled with a FRET-compatible dye. The optimized HTS assay yielded 109 potential inhibitors of CSR3 out of 6,620 compounds tested from different small-molecule libraries. The three best inhibitor candidates were validated with a dose-response assay. In addition, a parallel screen of the selected candidates was carried out for a similar class 1 RNase III enzyme from Escherichia coli (EcR3), and this screen yielded a different set of inhibitors. Thus, our results show that the CSR3 and EcR3 enzymes were inhibited by distinct types of molecules, indicating that this HTS assay could be widely applied in drug discovery of class 1 RNase III enzymes.
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Affiliation(s)
- Linping Wang
- Department of Agricultural SciencesUniversity of HelsinkiHelsinkiFinland
| | - Jani Saarela
- Institute for Molecular Medicine FinlandUniversity of HelsinkiHelsinkiFinland
| | - Sylvain Poque
- Department of Agricultural SciencesUniversity of HelsinkiHelsinkiFinland
| | - Jari P.T. Valkonen
- Department of Agricultural SciencesUniversity of HelsinkiHelsinkiFinland
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Schihada H, Ma X, Zabel U, Vischer HF, Schulte G, Leurs R, Pockes S, Lohse MJ. Development of a Conformational Histamine H 3 Receptor Biosensor for the Synchronous Screening of Agonists and Inverse Agonists. ACS Sens 2020; 5:1734-1742. [PMID: 32397705 PMCID: PMC7325232 DOI: 10.1021/acssensors.0c00397] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
![]()
The
histamine H3 receptor (H3R) represents
a highly attractive drug target for the treatment of various central
nervous system disorders, but the discovery of novel H3R targeting compounds relies on the assessment of highly amplified
intracellular signaling events that do not only reflect H3R modulation and carry the risk of high false-positive and -negative
screening rates. To address these limitations, we designed an intramolecular
H3R biosensor based on the principle of bioluminescence
resonance energy transfer (BRET) that reports the receptor’s
real-time conformational dynamics and provides an advanced tool to
screen for both H3R agonists and inverse agonists in a
live cell screening-compatible assay format. This conformational G-protein-coupled
receptor (GPCR) sensor allowed us to characterize the pharmacological
properties of known and new H3 receptor ligands with unprecedented
accuracy. Interestingly, we found that one newly developed H3 receptor ligand possesses even stronger inverse agonistic activity
than reference H3R inverse agonists including the current
gold standard pitolisant. Taken together, we describe here the design
and validation of the first screening-compatible H3R conformational
biosensor that will aid in the discovery of novel H3R ligands
and can be employed to gain deeper insights into the (in-)activation
mechanism of this highly attractive drug target.
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Affiliation(s)
- Hannes Schihada
- Section of Receptor Biology & Signaling, Dept. Physiology & Pharmacology, Karolinska Institutet, Stockholm 171 77, Sweden
- Institute of Pharmacology and Toxicology and Rudolf Virchow Center, University of Würzburg, Würzburg 97070, Germany
| | - Xiaoyuan Ma
- Amsterdam Institute for Molecules, Medicines and Systems, Division of Medicinal Chemistry, Faculty of Science, Vrije Universiteit Amsterdam, Amsterdam 1081 HV, The Netherlands
| | - Ulrike Zabel
- Institute of Pharmacology and Toxicology and Rudolf Virchow Center, University of Würzburg, Würzburg 97070, Germany
| | - Henry F. Vischer
- Amsterdam Institute for Molecules, Medicines and Systems, Division of Medicinal Chemistry, Faculty of Science, Vrije Universiteit Amsterdam, Amsterdam 1081 HV, The Netherlands
| | - Gunnar Schulte
- Section of Receptor Biology & Signaling, Dept. Physiology & Pharmacology, Karolinska Institutet, Stockholm 171 77, Sweden
| | - Rob Leurs
- Amsterdam Institute for Molecules, Medicines and Systems, Division of Medicinal Chemistry, Faculty of Science, Vrije Universiteit Amsterdam, Amsterdam 1081 HV, The Netherlands
| | - Steffen Pockes
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, Regensburg 93053, Germany
| | - Martin J. Lohse
- Institute of Pharmacology and Toxicology and Rudolf Virchow Center, University of Würzburg, Würzburg 97070, Germany
- ISAR Bioscience, Planegg 82152, Germany
- Max Delbrück Center for Molecular Medicine, Berlin 13125, Germany
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Pamula F, Mühle J, Blanc A, Nehmé R, Edwards PC, Tate CG, Tsai CJ. Strategic Screening and Characterization of the Visual GPCR-mini-G Protein Signaling Complex for Successful Crystallization. J Vis Exp 2020. [PMID: 32225143 PMCID: PMC7250641 DOI: 10.3791/60747] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The key to determining crystal structures of membrane protein complexes is the quality of the sample prior to crystallization. In particular, the choice of detergent is critical, because it affects both the stability and monodispersity of the complex. We recently determined the crystal structure of an active state of bovine rhodopsin coupled to an engineered G protein, mini-Go, at 3.1 Å resolution. Here, we detail the procedure for optimizing the preparation of the rhodopsin–mini-Go complex. Dark-state rhodopsin was prepared in classical and neopentyl glycol (NPG) detergents, followed by complex formation with mini-Go under light exposure. The stability of the rhodopsin was assessed by ultraviolet-visible (UV-VIS) spectroscopy, which monitors the reconstitution into rhodopsin of the light-sensitive ligand, 9-cis retinal. Automated size-exclusion chromatography (SEC) was used to characterize the monodispersity of rhodopsin and the rhodopsin–mini-Go complex. SDS-polyacrylamide electrophoresis (SDS-PAGE) confirmed the formation of the complex by identifying a 1:1 molar ratio between rhodopsin and mini-Go after staining the gel with Coomassie blue. After cross-validating all this analytical data, we eliminated unsuitable detergents and continued with the best candidate detergent for large-scale preparation and crystallization. An additional problem arose from the heterogeneity of N-glycosylation. Heterologously-expressed rhodopsin was observed on SDS-PAGE to have two different N-glycosylated populations, which would probably have hindered crystallogenesis. Therefore, different deglycosylation enzymes were tested, and endoglycosidase F1 (EndoF1) produced rhodopsin with a single species of N-glycosylation. With this strategic pipeline for characterizing protein quality, preparation of the rhodopsin–mini-Go complex was optimized to deliver the crystal structure. This was only the third crystal structure of a GPCR–G protein signaling complex. This approach can also be generalized for other membrane proteins and their complexes to facilitate sample preparation and structure determination.
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Affiliation(s)
- Filip Pamula
- Laboratory of Biomolecular Research, Paul Scherrer Institute; Department of Biology, ETH Zürich;
| | - Jonas Mühle
- Laboratory of Biomolecular Research, Paul Scherrer Institute
| | - Alain Blanc
- Center for Radiopharmaceutical Sciences, Paul Scherrer Institute
| | - Rony Nehmé
- Laboratory of Molecular Biology, Medical Research Council
| | | | | | - Ching-Ju Tsai
- Laboratory of Biomolecular Research, Paul Scherrer Institute;
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Maares M, Haase H. A Guide to Human Zinc Absorption: General Overview and Recent Advances of In Vitro Intestinal Models. Nutrients 2020; 12:E762. [PMID: 32183116 PMCID: PMC7146416 DOI: 10.3390/nu12030762] [Citation(s) in RCA: 138] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 02/23/2020] [Accepted: 03/09/2020] [Indexed: 12/17/2022] Open
Abstract
Zinc absorption in the small intestine is one of the main mechanisms regulating the systemic homeostasis of this essential trace element. This review summarizes the key aspects of human zinc homeostasis and distribution. In particular, current knowledge on human intestinal zinc absorption and the influence of diet-derived factors on bioaccessibility and bioavailability as well as intrinsic luminal and basolateral factors with an impact on zinc uptake are discussed. Their investigation is increasingly performed using in vitro cellular intestinal models, which are continually being refined and keep gaining importance for studying zinc uptake and transport via the human intestinal epithelium. The vast majority of these models is based on the human intestinal cell line Caco-2 in combination with other relevant components of the intestinal epithelium, such as mucin-secreting goblet cells and in vitro digestion models, and applying improved compositions of apical and basolateral media to mimic the in vivo situation as closely as possible. Particular emphasis is placed on summarizing previous applications as well as key results of these models, comparing their results to data obtained in humans, and discussing their advantages and limitations.
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Affiliation(s)
- Maria Maares
- Technische Universität Berlin, Chair of Food Chemistry and Toxicology, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Hajo Haase
- Technische Universität Berlin, Chair of Food Chemistry and Toxicology, Straße des 17. Juni 135, 10623 Berlin, Germany
- TraceAge-DFG Research Unit on Interactions of Essential Trace Elements in Healthy and Diseased Elderly, D-13353 Potsdam-Berlin-Jena, Germany
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Straightforward Protein-Protein Interaction Interface Mapping via Random Mutagenesis and Mammalian Protein Protein Interaction Trap (MAPPIT). Int J Mol Sci 2019; 20:ijms20092058. [PMID: 31027327 PMCID: PMC6539206 DOI: 10.3390/ijms20092058] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 04/08/2019] [Accepted: 04/13/2019] [Indexed: 01/18/2023] Open
Abstract
The MAPPIT (mammalian protein protein interaction trap) method allows high-throughput detection of protein interactions by very simple co-transfection of three plasmids in HEK293T cells, followed by a luciferase readout. MAPPIT detects a large percentage of all protein interactions, including those requiring posttranslational modifications and endogenous or exogenous ligands. Here, we present a straightforward method that allows detailed mapping of interaction interfaces via MAPPIT. The method provides insight into the interaction mechanism and reveals how this is affected by disease-associated mutations. By combining error-prone polymerase chain reaction (PCR) for random mutagenesis, 96-well DNA prepping, Sanger sequencing, and MAPPIT via 384-well transfections, we test the effects of a large number of mutations of a selected protein on its protein interactions. The entire screen takes less than three months and interactions with multiple partners can be studied in parallel. The effect of mutations on the MAPPIT readout is mapped on the protein structure, allowing unbiased identification of all putative interaction sites. We have thus far analysed 6 proteins and mapped their interfaces for 16 different interaction partners. Our method is broadly applicable as the required tools are simple and widely available.
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36
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Sakyiamah MM, Nomura W, Kobayakawa T, Tamamura H. Development of a NanoBRET-Based Sensitive Screening Method for CXCR4 Ligands. Bioconjug Chem 2019; 30:1442-1450. [DOI: 10.1021/acs.bioconjchem.9b00182] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Maxwell M. Sakyiamah
- Department of Medicinal Chemistry, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), 2-3-10 Kandasurugada, Chiyoda-ku, Tokyo 101-0062, Japan
- Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Wataru Nomura
- Department of Medicinal Chemistry, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), 2-3-10 Kandasurugada, Chiyoda-ku, Tokyo 101-0062, Japan
| | - Takuya Kobayakawa
- Department of Medicinal Chemistry, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), 2-3-10 Kandasurugada, Chiyoda-ku, Tokyo 101-0062, Japan
| | - Hirokazu Tamamura
- Department of Medicinal Chemistry, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), 2-3-10 Kandasurugada, Chiyoda-ku, Tokyo 101-0062, Japan
- Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
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37
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Wang Y, Zhang Y, Wang J, Liang XJ. Aggregation-induced emission (AIE) fluorophores as imaging tools to trace the biological fate of nano-based drug delivery systems. Adv Drug Deliv Rev 2019; 143:161-176. [PMID: 30529308 DOI: 10.1016/j.addr.2018.12.004] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Revised: 10/18/2018] [Accepted: 12/03/2018] [Indexed: 01/10/2023]
Abstract
The vigorous development of nanotechnology has been accompanied by an equally strong interest and research efforts in nano-based drug delivery systems (NDDSs). However, only a few NDDSs have been translated into clinic thus far. One of the important hurdles is the lack of tools to comprehensively and directly trace the biological fate of NDDSs. Recently, aggregation-induced emission (AIE) fluorophores have emerged as attractive bioimaging tools due to flexible controllability, negligible toxicity and superior photostability. Herein, we recapitulate the current advances in the application of AIE fluorophores to monitor NDDSs both in vitro and in vivo. Particularly, we discuss the cellular fates of self-indicating and stimuli-responsive NDDSs with AIE fluorophores. Moreover, we highlight the in vivo application of AIE agents on the long-term tracking of therapeutics and the multi-modal monitoring of diagnostics in NDDSs. Challenges and opportunities in AIE-guided exploration of NDDSs are also discussed in detail.
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Affiliation(s)
- Yufei Wang
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Chinese Academy of Sciences, National Center for Nanoscience and Technology of China, Beijing, 100190, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuxuan Zhang
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Chinese Academy of Sciences, National Center for Nanoscience and Technology of China, Beijing, 100190, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jinjin Wang
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Chinese Academy of Sciences, National Center for Nanoscience and Technology of China, Beijing, 100190, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xing-Jie Liang
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Chinese Academy of Sciences, National Center for Nanoscience and Technology of China, Beijing, 100190, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
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38
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Cui Y, Zhang X, Yu M, Zhu Y, Xing J, Lin J. Techniques for detecting protein-protein interactions in living cells: principles, limitations, and recent progress. SCIENCE CHINA-LIFE SCIENCES 2019; 62:619-632. [DOI: 10.1007/s11427-018-9500-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Accepted: 02/12/2019] [Indexed: 01/07/2023]
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39
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Bery N, Rabbitts TH. Bioluminescence Resonance Energy Transfer 2 (BRET2)-Based RAS Biosensors to Characterize RAS Inhibitors. ACTA ACUST UNITED AC 2019; 83:e83. [PMID: 30768855 DOI: 10.1002/cpcb.83] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Protein-protein interactions (PPIs) are principle biological processes that control normal cell growth, differentiation, and homeostasis but are also crucial in diseases such as malignancy, neuropathy, and infection. Despite the importance of PPIs in biology, this target class has been very challenging to convert to therapeutics. In the last decade, much progress has been made in the inhibition of PPIs involved in diseases, but many remain difficult such as RAS-effector interactions in cancers. We describe here a protocol for using Bioluminescence Resonance Energy Transfer 2 (BRET2)-based RAS biosensors to detect and characterize RAS PPI inhibition by macromolecules and small molecules. This method could be extended to any other small GTPases or any other PPIs of interest. © 2019 by John Wiley & Sons, Inc.
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Affiliation(s)
- Nicolas Bery
- Weatherall Institute of Molecular Medicine, MRC Molecular Haematology Unit, University of Oxford, John Radcliffe Hospital, Headington, Oxford, United Kingdom
| | - Terence H Rabbitts
- Weatherall Institute of Molecular Medicine, MRC Molecular Haematology Unit, University of Oxford, John Radcliffe Hospital, Headington, Oxford, United Kingdom
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40
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Struk S, Jacobs A, Sánchez Martín-Fontecha E, Gevaert K, Cubas P, Goormachtig S. Exploring the protein-protein interaction landscape in plants. PLANT, CELL & ENVIRONMENT 2019; 42:387-409. [PMID: 30156707 DOI: 10.1111/pce.13433] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 08/16/2018] [Indexed: 05/24/2023]
Abstract
Protein-protein interactions (PPIs) represent an essential aspect of plant systems biology. Identification of key protein players and their interaction networks provide crucial insights into the regulation of plant developmental processes and into interactions of plants with their environment. Despite the great advance in the methods for the discovery and validation of PPIs, still several challenges remain. First, the PPI networks are usually highly dynamic, and the in vivo interactions are often transient and difficult to detect. Therefore, the properties of the PPIs under study need to be considered to select the most suitable technique, because each has its own advantages and limitations. Second, besides knowledge on the interacting partners of a protein of interest, characteristics of the interaction, such as the spatial or temporal dynamics, are highly important. Hence, multiple approaches have to be combined to obtain a comprehensive view on the PPI network present in a cell. Here, we present the progress in commonly used methods to detect and validate PPIs in plants with a special emphasis on the PPI features assessed in each approach and how they were or can be used for the study of plant interactions with their environment.
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Affiliation(s)
- Sylwia Struk
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Anse Jacobs
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
- Department of Biochemistry, Ghent University, Ghent, Belgium
- Center for Medical Biotechnology, VIB, Ghent, Belgium
| | - Elena Sánchez Martín-Fontecha
- Plant Molecular Genetics Department, Centro Nacional de Biotecnología (CSIC), Campus Universidad Autónoma de Madrid, Madrid, Spain
| | - Kris Gevaert
- Department of Biochemistry, Ghent University, Ghent, Belgium
- Center for Medical Biotechnology, VIB, Ghent, Belgium
| | - Pilar Cubas
- Plant Molecular Genetics Department, Centro Nacional de Biotecnología (CSIC), Campus Universidad Autónoma de Madrid, Madrid, Spain
| | - Sofie Goormachtig
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
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Yakubu RR, Nieves E, Weiss LM. The Methods Employed in Mass Spectrometric Analysis of Posttranslational Modifications (PTMs) and Protein-Protein Interactions (PPIs). ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1140:169-198. [PMID: 31347048 DOI: 10.1007/978-3-030-15950-4_10] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Mass Spectrometry (MS) has revolutionized the way we study biomolecules, especially proteins, their interactions and posttranslational modifications (PTM). As such MS has established itself as the leading tool for the analysis of PTMs mainly because this approach is highly sensitive, amenable to high throughput and is capable of assigning PTMs to specific sites in the amino acid sequence of proteins and peptides. Along with the advances in MS methodology there have been improvements in biochemical, genetic and cell biological approaches to mapping the interactome which are discussed with consideration for both the practical and technical considerations of these techniques. The interactome of a species is generally understood to represent the sum of all potential protein-protein interactions. There are still a number of barriers to the elucidation of the human interactome or any other species as physical contact between protein pairs that occur by selective molecular docking in a particular spatiotemporal biological context are not easily captured and measured.PTMs massively increase the complexity of organismal proteomes and play a role in almost all aspects of cell biology, allowing for fine-tuning of protein structure, function and localization. There are an estimated 300 PTMS with a predicted 5% of the eukaryotic genome coding for enzymes involved in protein modification, however we have not yet been able to reliably map PTM proteomes due to limitations in sample preparation, analytical techniques, data analysis, and the substoichiometric and transient nature of some PTMs. Improvements in proteomic and mass spectrometry methods, as well as sample preparation, have been exploited in a large number of proteome-wide surveys of PTMs in many different organisms. Here we focus on previously published global PTM proteome studies in the Apicomplexan parasites T. gondii and P. falciparum which offer numerous insights into the abundance and function of each of the studied PTM in the Apicomplexa. Integration of these datasets provide a more complete picture of the relative importance of PTM and crosstalk between them and how together PTM globally change the cellular biology of the Apicomplexan protozoa. A multitude of techniques used to investigate PTMs, mostly techniques in MS-based proteomics, are discussed for their ability to uncover relevant biological function.
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Affiliation(s)
- Rama R Yakubu
- Department of Pathology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Edward Nieves
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA.,Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Louis M Weiss
- Department of Pathology, Albert Einstein College of Medicine, Bronx, NY, USA. .,Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, USA.
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42
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Laschet C, Dupuis N, Hanson J. A dynamic and screening-compatible nanoluciferase-based complementation assay enables profiling of individual GPCR-G protein interactions. J Biol Chem 2018; 294:4079-4090. [PMID: 30593506 DOI: 10.1074/jbc.ra118.006231] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 12/27/2018] [Indexed: 12/14/2022] Open
Abstract
G protein-coupled receptors (GPCRs) are currently the target of more than 30% of the marketed medicines. However, there is an important medical need for ligands with improved pharmacological activities on validated drug targets. Moreover, most of these ligands remain poorly characterized, notably because of a lack of pharmacological tools. Thus, there is an important demand for innovative assays that can detect and drive the design of compounds with novel or improved pharmacological properties. In particular, a functional and screening-compatible GPCR-G protein interaction assay is still unavailable. Here, we report on a nanoluciferase-based complementation technique to detect ligands that promote a GPCR-G protein interaction. We demonstrate that our system can be used to profile compounds with regard to the G proteins they activate through a given GPCR. Furthermore, we established a proof of applicability of screening for distinct G proteins on dopamine receptor D2 whose differential coupling to Gαi/o family members has been extensively studied. In a D2-Gαi1 versus D2-Gαo screening, we retrieved five agonists that are currently being used in antiparkinsonian medications. We determined that in this assay, piribedil and pergolide are full agonists for the recruitment of Gαi1 but are partial agonists for Gαo, that the agonist activity of ropinirole is biased in favor of Gαi1 recruitment, and that the agonist activity of apomorphine is biased for Gαo We propose that this newly developed assay could be used to develop molecules that selectively modulate a particular G protein pathway.
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Affiliation(s)
- Céline Laschet
- From the Laboratory of Molecular Pharmacology, GIGA-Molecular Biology of Diseases, University of Liège, 4000 Liège and
| | - Nadine Dupuis
- From the Laboratory of Molecular Pharmacology, GIGA-Molecular Biology of Diseases, University of Liège, 4000 Liège and
| | - Julien Hanson
- From the Laboratory of Molecular Pharmacology, GIGA-Molecular Biology of Diseases, University of Liège, 4000 Liège and .,the Laboratory of Medicinal Chemistry, CIRM-Drug Target and Lead Discovery, University of Liège, Liège CHU, B34 (+4), B-4000 Liège, Belgium
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43
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Li J, Liu S, Sun L, Li W, Zhang SY, Yang S, Li J, Yang HH. Amplified Visualization of Protein-Specific Glycosylation in Zebrafish via Proximity-Induced Hybridization Chain Reaction. J Am Chem Soc 2018; 140:16589-16595. [DOI: 10.1021/jacs.8b08442] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jingying Li
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350116, P. R. China
| | - Shuya Liu
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350116, P. R. China
| | - Liqin Sun
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350116, P. R. China
| | - Wei Li
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350116, P. R. China
| | - Su-Yun Zhang
- Department of Medical Oncology, Fujian Medical University Union Hospital, Fuzhou 350001, P. R. China
| | - Sheng Yang
- Department of Medical Oncology, Fujian Medical University Union Hospital, Fuzhou 350001, P. R. China
| | - Juan Li
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350116, P. R. China
| | - Huang-Hao Yang
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350116, P. R. China
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350116, P. R. China
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44
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Guder P, Lotz-Havla AS, Woidy M, Reiß DD, Danecka MK, Schatz UA, Becker M, Ensenauer R, Pagel P, Büttner L, Muntau AC, Gersting SW. Isoform-specific domain organization determines conformation and function of the peroxisomal biogenesis factor PEX26. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2018; 1866:518-531. [PMID: 30366024 DOI: 10.1016/j.bbamcr.2018.10.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 10/11/2018] [Accepted: 10/18/2018] [Indexed: 10/28/2022]
Abstract
Peroxisomal biogenesis factor PEX26 is a membrane anchor for the multi-subunit PEX1-PEX6 protein complex that controls ubiquitination and dislocation of PEX5 cargo receptors for peroxisomal matrix protein import. PEX26 associates with the peroxisomal translocation pore via PEX14 and a splice variant (PEX26Δex5) of unknown function has been reported. Here, we demonstrate PEX26 homooligomerization mediated by two heptad repeat domains adjacent to the transmembrane domain. We show that isoform-specific domain organization determines PEX26 oligomerization and impacts peroxisomal β-oxidation and proliferation. PEX26 and PEX26Δex5 displayed different patterns of interaction with PEX2-PEX10 or PEX13-PEX14 complexes, which relate to distinct pre-peroxisomes in the de novo synthesis pathway. Our data support an alternative PEX14-dependent mechanism of peroxisomal membrane association for the splice variant, which lacks a transmembrane domain. Structure-function relationships of PEX26 isoforms explain an extended function in peroxisomal homeostasis and these findings may improve our understanding of the broad phenotype of PEX26-associated human disorders.
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Affiliation(s)
- Philipp Guder
- University Children's Research@Kinder-UKE, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; Children's Hospital, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Amelie S Lotz-Havla
- Dr. von Hauner Children's Hospital, Ludwig-Maximilians-University, 80337 Munich, Germany
| | - Mathias Woidy
- University Children's Research@Kinder-UKE, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; Children's Hospital, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Dunja D Reiß
- Dr. von Hauner Children's Hospital, Ludwig-Maximilians-University, 80337 Munich, Germany
| | - Marta K Danecka
- University Children's Research@Kinder-UKE, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Ulrich A Schatz
- Department for Medical Genetics, Molecular and Clinical Pharmacology, Medical University Innsbruck, 6020 Innsbruck, Austria
| | - Marc Becker
- Dr. von Hauner Children's Hospital, Ludwig-Maximilians-University, 80337 Munich, Germany; Labor Becker Olgemöller und Kollegen, 81671 Munich, Germany
| | - Regina Ensenauer
- Dr. von Hauner Children's Hospital, Ludwig-Maximilians-University, 80337 Munich, Germany; Experimental Pediatrics, Department of General Pediatrics, Neonatology and Pediatric Cardiology, University Children's Hospital, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Philipp Pagel
- Lehrstuhl für Genomorientierte Bioinformatik, Technische Universität, 85350 Freising, Germany; numares GmbH, Josef-Engert-Str. 9, 93053 Regensburg, Germany
| | - Lars Büttner
- Dr. von Hauner Children's Hospital, Ludwig-Maximilians-University, 80337 Munich, Germany
| | - Ania C Muntau
- Children's Hospital, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Søren W Gersting
- University Children's Research@Kinder-UKE, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; Children's Hospital, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany.
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Exploring Protein⁻Protein Interaction in the Study of Hormone-Dependent Cancers. Int J Mol Sci 2018; 19:ijms19103173. [PMID: 30326622 PMCID: PMC6213999 DOI: 10.3390/ijms19103173] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 10/09/2018] [Accepted: 10/10/2018] [Indexed: 12/20/2022] Open
Abstract
Estrogen receptors promote target gene transcription when they form a dimer, in which two identical (homodimer) or different (heterodimer) proteins are bound to each other. In hormone-dependent cancers, hormone receptor dimerization plays pivotal roles, not only in the pathogenesis or development of the tumors, but also in the development of therapeutic resistance. Protein–protein interactions (PPIs), including dimerization and complex formation, have been also well-known to be required for proteins to exert their functions. The methods which could detect PPIs are genetic engineering (i.e., resonance energy transfer) and/or antibody technology (i.e., co-immunoprecipitation) using cultured cells. In addition, visualization of the target proteins in tissues can be performed using antigen–antibody reactions, as in immunohistochemistry. Furthermore, development of microscopic techniques (i.e., electron microscopy and confocal laser microscopy) has made it possible to visualize intracellular and/or intranuclear organelles. We have recently reported the visualization of estrogen receptor dimers in breast cancer tissues by using the in situ proximity ligation assay (PLA). PLA was developed along the lines of antibody technology development, and this assay has made it possible to visualize PPIs in archival tissue specimens. Localization of PPI in organelles has also become possible using super-resolution microscopes exceeding the resolution limit of conventional microscopes. Therefore, in this review, we summarize the methodologies used for studying PPIs in both cells and tissues, and review the recently reported studies on PPIs of hormones.
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46
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Orphan Nuclear Receptors in Colorectal Cancer. Pathol Oncol Res 2018; 24:815-819. [DOI: 10.1007/s12253-018-0440-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 05/30/2018] [Indexed: 12/30/2022]
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47
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Robichaux WG, Cheng X. Intracellular cAMP Sensor EPAC: Physiology, Pathophysiology, and Therapeutics Development. Physiol Rev 2018; 98:919-1053. [PMID: 29537337 PMCID: PMC6050347 DOI: 10.1152/physrev.00025.2017] [Citation(s) in RCA: 131] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 09/05/2017] [Accepted: 09/06/2017] [Indexed: 12/13/2022] Open
Abstract
This review focuses on one family of the known cAMP receptors, the exchange proteins directly activated by cAMP (EPACs), also known as the cAMP-regulated guanine nucleotide exchange factors (cAMP-GEFs). Although EPAC proteins are fairly new additions to the growing list of cAMP effectors, and relatively "young" in the cAMP discovery timeline, the significance of an EPAC presence in different cell systems is extraordinary. The study of EPACs has considerably expanded the diversity and adaptive nature of cAMP signaling associated with numerous physiological and pathophysiological responses. This review comprehensively covers EPAC protein functions at the molecular, cellular, physiological, and pathophysiological levels; and in turn, the applications of employing EPAC-based biosensors as detection tools for dissecting cAMP signaling and the implications for targeting EPAC proteins for therapeutic development are also discussed.
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Affiliation(s)
- William G Robichaux
- Department of Integrative Biology and Pharmacology, Texas Therapeutics Institute, The Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center , Houston, Texas
| | - Xiaodong Cheng
- Department of Integrative Biology and Pharmacology, Texas Therapeutics Institute, The Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center , Houston, Texas
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48
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Detection and Quantitative Analysis of Dynamic GPCRs Interactions Using Flow Cytometry-Based FRET. RECEPTOR-RECEPTOR INTERACTIONS IN THE CENTRAL NERVOUS SYSTEM 2018. [DOI: 10.1007/978-1-4939-8576-0_14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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49
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Slavcev RA, Sum CH, St Jean J, Huh H, Nafissi N. Specific Systems for Evaluation. EXPERIENTIA SUPPLEMENTUM (2012) 2018; 110:99-123. [PMID: 30536228 DOI: 10.1007/978-3-319-78259-1_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Fluorescent-based visualization techniques have long been used to monitor biological activity. This chapter explores the delivery of reporter genes as a means to assay and track activity in biological systems. Bioluminescence is the production of light due to biochemical processes. By encoding genes for bioluminescence, biological processes can be visualized based on gene expression. This chapter also discusses the primary applications of bioluminescence as seen through bioluminescent imaging techniques, flow cytometry, and PCR-based methods of gene detection. These techniques are described in terms of researching gene expression, cancer therapy, and protein interactions.
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Affiliation(s)
| | - Chi Hong Sum
- University of Waterloo, School of Pharmacy, Waterloo, ON, Canada
| | - Jesse St Jean
- University of Waterloo, School of Pharmacy, Waterloo, ON, Canada
| | - Haein Huh
- University of Waterloo, School of Pharmacy, Waterloo, ON, Canada
| | - Nafiseh Nafissi
- University of Waterloo, School of Pharmacy, Waterloo, ON, Canada
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50
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Gondoin A, Hampe C, Eudes R, Fayolle C, Pierre-Eugène C, Miteva M, Villoutreix BO, Charnay-Pouget F, Aitken DJ, Issad T, Burnol AF. Identification of insulin-sensitizing molecules acting by disrupting the interaction between the Insulin Receptor and Grb14. Sci Rep 2017; 7:16901. [PMID: 29203791 PMCID: PMC5715071 DOI: 10.1038/s41598-017-17122-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 11/22/2017] [Indexed: 01/07/2023] Open
Abstract
Metabolic diseases are characterized by a decreased action of insulin. During the course of the disease, usual treatments frequently fail and patients are finally submitted to insulinotherapy. There is thus a need for innovative therapeutic strategies to improve insulin action. Growth factor receptor-bound protein 14 (Grb14) is a molecular adapter that specifically binds to the activated insulin receptor (IR) and inhibits its tyrosine kinase activity. Molecules disrupting Grb14-IR binding are therefore potential insulin-sensitizing agents. We used Structure-Based Virtual Ligand Screening to generate a list of 1000 molecules predicted to hinder Grb14-IR binding. Using an acellular bioluminescence resonance energy transfer (BRET) assay, we identified, out of these 1000 molecules, 3 compounds that inhibited Grb14-IR interaction. Their inhibitory effect on insulin-induced Grb14-IR interaction was confirmed in co-immunoprecipitation experiments. The more efficient molecule (C8) was further characterized. C8 increased downstream Ras-Raf and PI3-kinase insulin signaling, as shown by BRET experiments in living cells. Moreover, C8 regulated the expression of insulin target genes in mouse primary hepatocytes. These results indicate that C8, by reducing Grb14-IR interaction, increases insulin signalling. The use of C8 as a lead compound should allow for the development of new molecules of potential therapeutic interest for the treatment of diabetes.
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Affiliation(s)
- Anaïs Gondoin
- Institut Cochin, Université Paris Descartes, CNRS (UMR8104), Paris, France.,INSERM, U1016, Paris, France
| | - Cornelia Hampe
- Institut Cochin, Université Paris Descartes, CNRS (UMR8104), Paris, France.,INSERM, U1016, Paris, France
| | - Richard Eudes
- Université Paris Diderot, Sorbonne-Paris-Cité, Inserm UMR-S 973, Molécules Thérapeutiques in silico, Paris, France
| | - Cyril Fayolle
- Institut Cochin, Université Paris Descartes, CNRS (UMR8104), Paris, France.,INSERM, U1016, Paris, France
| | - Cécile Pierre-Eugène
- Institut Cochin, Université Paris Descartes, CNRS (UMR8104), Paris, France.,INSERM, U1016, Paris, France
| | - Maria Miteva
- Université Paris Diderot, Sorbonne-Paris-Cité, Inserm UMR-S 973, Molécules Thérapeutiques in silico, Paris, France
| | - Bruno O Villoutreix
- Université Paris Diderot, Sorbonne-Paris-Cité, Inserm UMR-S 973, Molécules Thérapeutiques in silico, Paris, France
| | - Florence Charnay-Pouget
- CP3A Organic Synthesis Group, ICMMO, UMR 8182, CNRS, Université Paris Sud, Université Paris Saclay, Orsay, France
| | - David J Aitken
- CP3A Organic Synthesis Group, ICMMO, UMR 8182, CNRS, Université Paris Sud, Université Paris Saclay, Orsay, France
| | - Tarik Issad
- Institut Cochin, Université Paris Descartes, CNRS (UMR8104), Paris, France. .,INSERM, U1016, Paris, France.
| | - Anne-Françoise Burnol
- Institut Cochin, Université Paris Descartes, CNRS (UMR8104), Paris, France. .,INSERM, U1016, Paris, France.
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