1
|
Kim SB, Furuta T, Thangudu S, Natarajan A, Paulmurugan R. Molecular Association Assay Systems for Imaging Protein-Protein Interactions in Mammalian Cells. BIOSENSORS 2025; 15:299. [PMID: 40422038 DOI: 10.3390/bios15050299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2025] [Revised: 04/22/2025] [Accepted: 04/25/2025] [Indexed: 05/28/2025]
Abstract
Molecular imaging probes play a pivotal role in assaying molecular events in various physiological systems. In this study, we demonstrate a new genre of bioluminescent probes for imaging protein-protein interactions (PPIs) in mammalian cells, named the molecular association assay (MAA) probe. The MAA probe is designed to be as simple as a full-length marine luciferase fused to a protein of interest with a flexible linker. This simple fusion protein alone surprisingly works by recognizing a specific ligand, interacting with a counterpart protein of the PPI, and developing bioluminescence (BL) in mammalian cells. We made use of an artificial intelligence (AI) tool to simulate the binding modes and working mechanisms. Our AlphaFold-based analysis on the binding mode suggests that the hinge region of the MAA probe is flexible before ligand binding but becomes stiff after ligand binding and protein association. The sensorial properties of representative MAA probes, FRB-ALuc23 and FRB-R86SG, are characterized with respect to the quantitative feature, BL spectrum, and in vivo tumor imaging using xenografted mice. Our AI-based simulation of the working mechanisms reveals that the association of MAA probes with the other proteins works in a way to facilitate the substrate's access to the active sites of the luciferase (ALuc23 or R86SG). We prove that the concept of MAA is generally applicable to other examples, such as the ALuc16- or R86SG-fused estrogen receptor ligand-binding domain (ER LBD). Considering the versatility of this conceptionally unique and distinctive molecular imaging probe compared to conventional ones, we are expecting the widespread application of these probes as a new imaging repertoire to determine PPIs in living organisms.
Collapse
Affiliation(s)
- Sung-Bae Kim
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba 305-8569, Japan
| | - Tadaomi Furuta
- School of Life Science and Technology, Institute of Science Tokyo, B-62 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
| | - Suresh Thangudu
- Molecular Imaging Program at Stanford, Bio-X Program, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Arutselvan Natarajan
- Molecular Imaging Program at Stanford, Bio-X Program, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Ramasamy Paulmurugan
- Molecular Imaging Program at Stanford, Bio-X Program, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| |
Collapse
|
2
|
Kim SB, Kamiya G, Furuta T, Maki SA. Coelenterazine Analogs for Bioassays and Molecular Imaging. SENSORS (BASEL, SWITZERLAND) 2025; 25:1651. [PMID: 40292719 PMCID: PMC11945097 DOI: 10.3390/s25061651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2025] [Revised: 02/28/2025] [Accepted: 03/05/2025] [Indexed: 04/30/2025]
Abstract
Coelenterazine (CTZ) is a common substrate of marine luciferases upon emission of bioluminescence (BL) in living organisms. Because CTZ works as a "luminophore" in the process of BL emission, the chemical modification has been centered for improving the optical properties of BL. In this review, we showcase recent advances in CTZ designs with unique functionalities. We first elucidate the light-emitting mechanisms of CTZ, and then focus on how the rational modification of CTZ analogs developed in recent years are connected to the development of unique functionalities even without luciferases, which include color tunability covering the visible region, specificity to various proteins (e.g., luciferase, albumin, and virus protein), and activatability to ions or reactive oxygen species (ROS) and anticancer drugs. This review provides new insights into the broad utilities of CTZ analogs with designed functionalities in bioassays and molecular imaging.
Collapse
Affiliation(s)
- Sung-Bae Kim
- Environmental Management Research Institute (EMRI), National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba 305-8569, Japan
| | - Genta Kamiya
- Department of Engineering Science, Graduate School of Informatics and Engineering, The University of Electro-Communications, Chofu 182-8585, Japan; (G.K.); (S.A.M.)
| | - Tadaomi Furuta
- School of Life Science and Technology, Institute of Science Tokyo, B-62 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan;
| | - Shojiro A. Maki
- Department of Engineering Science, Graduate School of Informatics and Engineering, The University of Electro-Communications, Chofu 182-8585, Japan; (G.K.); (S.A.M.)
| |
Collapse
|
3
|
Fan R, Aranko AS. Catcher/Tag Toolbox: Biomolecular Click-Reactions For Protein Engineering Beyond Genetics. Chembiochem 2024; 25:e202300600. [PMID: 37851860 DOI: 10.1002/cbic.202300600] [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: 08/28/2023] [Revised: 10/18/2023] [Accepted: 10/18/2023] [Indexed: 10/20/2023]
Abstract
Manipulating protein architectures beyond genetic control has attracted widespread attention. Catcher/Tag systems enable highly specific conjugation of proteins in vivo and in vitro via an isopeptide-bond. They provide efficient, robust, and irreversible strategies for protein conjugation and are simple yet powerful tools for a variety of applications in enzyme industry, vaccines, biomaterials, and cellular applications. Here we summarize recent development of the Catcher/Tag toolbox with a particular emphasis on the design of Catcher/Tag pairs targeted for specific applications. We cover the current limitations of the Catcher/Tag systems and discuss the pH sensitivity of the reactions. Finally, we conclude some of the future directions in the development of this versatile protein conjugation method and envision that improved control over inducing the ligation reaction will further broaden the range of applications.
Collapse
Affiliation(s)
- Ruxia Fan
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, P.O. Box 16100, 02150, Espoo, Finland
| | - A Sesilja Aranko
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, P.O. Box 16100, 02150, Espoo, Finland
| |
Collapse
|
4
|
Liu Y, Zhang X, Zhang P, He T, Zhang W, Ma D, Li P, Chen J. A high-throughput Gaussia luciferase reporter assay for screening potential gasdermin E activators against pancreatic cancer. Acta Pharm Sin B 2023; 13:4253-4272. [PMID: 37799380 PMCID: PMC10548051 DOI: 10.1016/j.apsb.2023.07.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 05/20/2023] [Accepted: 06/15/2023] [Indexed: 10/07/2023] Open
Abstract
It is discovered that activated caspase-3 tends to induce apoptosis in gasdermin E (GSDME)-deficient cells, but pyroptosis in GSDME-sufficient cells. The high GSDME expression and apoptosis resistance of pancreatic ductal adenocarcinoma (PDAC) cells shed light on another attractive strategy for PDAC treatment by promoting pyroptosis. Here we report a hGLuc-hGSDME-PCA system for high-throughput screening of potential GSDME activators against PDAC. This screening system neatly quantifies the oligomerization of GSDME-N to characterize whether pyroptosis occurs under the stimulation of chemotherapy drugs. Based on this system, ponatinib and perifosine are screened out from the FDA-approved anti-cancer drug library containing 106 compounds. Concretely, they exhibit the most potent luminescent activity and cause drastic pyroptosis in PDAC cells. Further, we demonstrate that perifosine suppresses pancreatic cancer by promoting pyroptosis via caspase-3/GSDME pathway both in vitro and in vivo. Collectively, this study reveals the great significance of hGLuc-hGSDME-PCA in identifying compounds triggering GSDME-dependent pyroptosis and developing promising therapeutic agents for PDAC.
Collapse
Affiliation(s)
- Yang Liu
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
- Department of Pharmacognosy, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, China
| | - Xiaowei Zhang
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
- Department of Pharmacognosy, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, China
| | - Ping Zhang
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
- Department of Pharmacognosy, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, China
| | - Tingting He
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
- Department of Pharmacognosy, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, China
| | - Weitao Zhang
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
- Department of Pharmacognosy, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, China
| | - Dingyuan Ma
- Department of Prenatal Diagnosis, Nanjing Maternity and Child Health Care Hospital, Women's Hospital of Nanjing Medical University, Nanjing 210004, China
| | - Ping Li
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
| | - Jun Chen
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
- Department of Pharmacognosy, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, China
| |
Collapse
|
5
|
Monti A, Vitagliano L, Caporale A, Ruvo M, Doti N. Targeting Protein-Protein Interfaces with Peptides: The Contribution of Chemical Combinatorial Peptide Library Approaches. Int J Mol Sci 2023; 24:7842. [PMID: 37175549 PMCID: PMC10178479 DOI: 10.3390/ijms24097842] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 04/22/2023] [Accepted: 04/23/2023] [Indexed: 05/15/2023] Open
Abstract
Protein-protein interfaces play fundamental roles in the molecular mechanisms underlying pathophysiological pathways and are important targets for the design of compounds of therapeutic interest. However, the identification of binding sites on protein surfaces and the development of modulators of protein-protein interactions still represent a major challenge due to their highly dynamic and extensive interfacial areas. Over the years, multiple strategies including structural, computational, and combinatorial approaches have been developed to characterize PPI and to date, several successful examples of small molecules, antibodies, peptides, and aptamers able to modulate these interfaces have been determined. Notably, peptides are a particularly useful tool for inhibiting PPIs due to their exquisite potency, specificity, and selectivity. Here, after an overview of PPIs and of the commonly used approaches to identify and characterize them, we describe and evaluate the impact of chemical peptide libraries in medicinal chemistry with a special focus on the results achieved through recent applications of this methodology. Finally, we also discuss the role that this methodology can have in the framework of the opportunities, and challenges that the application of new predictive approaches based on artificial intelligence is generating in structural biology.
Collapse
Affiliation(s)
- Alessandra Monti
- Institute of Biostructures and Bioimaging (IBB), National Research Council (CNR), 80131 Napoli, Italy; (A.M.); (L.V.); (M.R.)
| | - Luigi Vitagliano
- Institute of Biostructures and Bioimaging (IBB), National Research Council (CNR), 80131 Napoli, Italy; (A.M.); (L.V.); (M.R.)
| | - Andrea Caporale
- Institute of Crystallography (IC), National Research Council (CNR), Strada Statale 14 km 163.5, Basovizza, 34149 Triese, Italy;
| | - Menotti Ruvo
- Institute of Biostructures and Bioimaging (IBB), National Research Council (CNR), 80131 Napoli, Italy; (A.M.); (L.V.); (M.R.)
| | - Nunzianna Doti
- Institute of Biostructures and Bioimaging (IBB), National Research Council (CNR), 80131 Napoli, Italy; (A.M.); (L.V.); (M.R.)
| |
Collapse
|
6
|
Kim SB, Furuta T, Kamiya G, Kitada N, Paulmurugan R, Maki SA. Bright Molecular Strain Probe Templates for Reporting Protein-Protein Interactions. SENSORS (BASEL, SWITZERLAND) 2023; 23:3498. [PMID: 37050557 PMCID: PMC10098686 DOI: 10.3390/s23073498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/20/2023] [Accepted: 03/22/2023] [Indexed: 06/19/2023]
Abstract
Imaging protein-protein interactions (PPIs) is a hot topic in molecular medicine in the postgenomic sequencing era. In the present study, we report bright and highly sensitive single-chain molecular strain probe templates which embed full-length Renilla luciferase 8.6-535SG (RLuc86SG) or Artificial luciferase 49 (ALuc49) as reporters. These reporters were deployed between FKBP-rapamycin binding domain (FRB) and FK506-binding protein (FKBP) as a PPI model. This unique molecular design was conceptualized to exploit molecular strains of the sandwiched reporters appended by rapamycin-triggered intramolecular PPIs. The ligand-sensing properties of the templates were maximized by interface truncations and substrate modulation. The highest fold intensities, 9.4 and 16.6, of the templates were accomplished with RLuc86SG and ALuc49, respectively. The spectra of the templates, according to substrates, revealed that the colors are tunable to blue, green, and yellow. The putative substrate-binding chemistry and the working mechanisms of the probes were computationally modeled in the presence or absence of rapamycin. Considering that the molecular strain probe templates are applicable to other PPI models, the present approach would broaden the scope of the bioassay toolbox, which harnesses the privilege of luciferase reporters and the unique concept of the molecular strain probes into bioassays and molecular imaging.
Collapse
Affiliation(s)
- Sung-Bae Kim
- Environmental Management Research Institute (EMRI), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8569, Japan
| | - Tadaomi Furuta
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Genta Kamiya
- Department of Engineering Science, Graduate School of Informatics and Engineering, The University of Electro-Communications, Chofu 182-8585, Japan
| | - Nobuo Kitada
- Department of Engineering Science, Graduate School of Informatics and Engineering, The University of Electro-Communications, Chofu 182-8585, Japan
| | - Ramasamy Paulmurugan
- Molecular Imaging Program at Stanford, Bio-X Program, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Shojiro A. Maki
- Department of Engineering Science, Graduate School of Informatics and Engineering, The University of Electro-Communications, Chofu 182-8585, Japan
| |
Collapse
|
7
|
Kattan RE, Ayesh D, Wang W. Analysis of affinity purification-related proteomic data for studying protein-protein interaction networks in cells. Brief Bioinform 2023; 24:bbad010. [PMID: 36682002 PMCID: PMC10025443 DOI: 10.1093/bib/bbad010] [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: 11/07/2022] [Revised: 12/22/2022] [Accepted: 01/02/2023] [Indexed: 01/23/2023] Open
Abstract
During intracellular signal transduction, protein-protein interactions (PPIs) facilitate protein complex assembly to regulate protein localization and function, which are critical for numerous cellular events. Over the years, multiple techniques have been developed to characterize PPIs to elucidate roles and regulatory mechanisms of proteins. Among them, the mass spectrometry (MS)-based interactome analysis has been increasing in popularity due to its unbiased and informative manner towards understanding PPI networks. However, with MS instrumentation advancing and yielding more data than ever, the analysis of a large amount of PPI-associated proteomic data to reveal bona fide interacting proteins become challenging. Here, we review the methods and bioinformatic resources that are commonly used in analyzing large interactome-related proteomic data and propose a simple guideline for identifying novel interacting proteins for biological research.
Collapse
Affiliation(s)
- Rebecca Elizabeth Kattan
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA
| | - Deena Ayesh
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA
| | - Wenqi Wang
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA
| |
Collapse
|
8
|
Sun M, Yuan F, Tang Y, Zou P, Lei X. Subcellular Interactomes Revealed by Merging APEX with Cross-Linking Mass Spectrometry. Anal Chem 2022; 94:14878-14888. [PMID: 36265550 DOI: 10.1021/acs.analchem.2c02116] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Subcellular protein-protein interactions (PPIs) are essential to understanding the mechanism of diverse cellular signaling events and the pathogenesis of diseases. Herein, we report an integrated APEX proximity labeling and chemical cross-linking coupled with mass spectrometry (CXMS) platform named APEX-CXMS for spatially resolved subcellular interactome profiling in a high-throughput manner. APEX proximity labeling rapidly captures subcellular proteomes, and the highly reactive chemical cross-linkers can capture weak and dynamic interactions globally without extra genetic manipulation. APEX-CXMS was first applied to mitochondria and identified 653 pairs of interprotein cross-links. Six pairs of new interactions were selected and verified by coimmunoprecipitation, the mammalian two-hybrid system, and surface plasmon resonance method. Besides, our approach was further applied to the nucleus, capturing 336 pairs of interprotein cross-links with approximately 94% nuclear specificity. APEX-CXMS thus provides a simple, fast, and general alternative to map diverse subcellular PPIs.
Collapse
Affiliation(s)
- Mengze Sun
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Feng Yuan
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Yuliang Tang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Peng Zou
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China.,PKU-IDG/McGovern Institute for Brain Research, Peking University, Beijing 100871, China.,Chinese Institute for Brain Research (CIBR), Beijing 102206, China
| | - Xiaoguang Lei
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China.,Institute for Cancer Research, Shenzhen Bay Laboratory, Shenzhen 518107, China
| |
Collapse
|
9
|
Jeremiah SS, Miyakawa K, Ryo A. Detecting SARS-CoV-2 neutralizing immunity: highlighting the potential of split nanoluciferase technology. J Mol Cell Biol 2022; 14:mjac023. [PMID: 35416249 PMCID: PMC9387144 DOI: 10.1093/jmcb/mjac023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 02/22/2022] [Accepted: 03/01/2022] [Indexed: 11/24/2022] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has progressed over 2 years since its onset causing significant health concerns all over the world and is currently curtailed by mass vaccination. Immunity acquired against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can be following either infection or vaccination. However, one can never be sure whether the acquired immunity is adequate to protect the individual from subsequent infection because of three important factors: individual variations in humoral response dynamics, waning of protective antibodies over time, and the emergence of immune escape mutants. Therefore, a test that can accurately differentiate the protected from the vulnerable is the need of the hour. The plaque reduction neutralization assay is the conventional gold standard test for estimating the titers of neutralizing antibodies that confer protection. However, it has got several drawbacks, which hinder the practical application of this test for wide-scale usage. Hence, various tests have been developed to detect protective immunity against SARS-CoV-2 that directly or indirectly assess the presence of neutralizing antibodies to SARS-CoV-2 in a lower biosafety setting. In this review, the pros and cons of the currently available assays are elaborated in detail and special focus is put on the scope of the novel split nanoluciferase technology for detecting SARS-CoV-2 neutralizing antibodies.
Collapse
Affiliation(s)
| | - Kei Miyakawa
- Department of Microbiology, Yokohama City University School of Medicine, Yokohama 236-0004, Japan
| | - Akihide Ryo
- Department of Microbiology, Yokohama City University School of Medicine, Yokohama 236-0004, Japan
| |
Collapse
|
10
|
Topcu E, Ridgeway NH, Biggar KK. PeSA 2.0: A software tool for peptide specificity analysis implementing positive and negative motifs and motif-based peptide scoring. Comput Biol Chem 2022; 101:107753. [PMID: 35998543 DOI: 10.1016/j.compbiolchem.2022.107753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 08/05/2022] [Accepted: 08/09/2022] [Indexed: 11/26/2022]
Abstract
There are a vast number of molecular interactions that occur at the cellular level. Among these molecular interactions, interactions between multiple proteins are a widely studied area of research due to the importance of these interactions in cellular function and their potential in drug development. PeSA is a desktop application developed to facilitate the in vitro peptide study analysis to predict protein-protein interactions. PeSA can effortlessly generate visual outputs like motifs, bar charts, and visual matrices. Our implementation of PeSA version 2.0 includes additional tools, including the ability to further score peptide lists for consensus amongst interactions. The software is also able to design de novo peptides based on sequence motifs (sequence generator), which can be used to help design additional experiments for motif validation. Further, the efficacy of the sequence generator was validated using the lysine methyltransferase, SETD8, to identify new substrates of methylation based on motif-based predictions developed using PeSA2.0.
Collapse
Affiliation(s)
- Emine Topcu
- Institute of Biochemistry and Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario K1N 5B6, Canada
| | - Nashira H Ridgeway
- Institute of Biochemistry and Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario K1N 5B6, Canada
| | - Kyle K Biggar
- Institute of Biochemistry and Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario K1N 5B6, Canada.
| |
Collapse
|
11
|
Xie VC, Styles MJ, Dickinson BC. Methods for the directed evolution of biomolecular interactions. Trends Biochem Sci 2022; 47:403-416. [PMID: 35427479 PMCID: PMC9022280 DOI: 10.1016/j.tibs.2022.01.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 12/27/2021] [Accepted: 01/13/2022] [Indexed: 02/06/2023]
Abstract
Noncovalent interactions between biomolecules such as proteins and nucleic acids coordinate all cellular processes through changes in proximity. Tools that perturb these interactions are and will continue to be highly valuable for basic and translational scientific endeavors. By taking cues from natural systems, such as the adaptive immune system, we can design directed evolution platforms that can generate proteins that bind to biomolecules of interest. In recent years, the platforms used to direct the evolution of biomolecular binders have greatly expanded the range of types of interactions one can evolve. Herein, we review recent advances in methods to evolve protein-protein, protein-RNA, and protein-DNA interactions.
Collapse
Affiliation(s)
| | - Matthew J Styles
- Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA
| | - Bryan C Dickinson
- Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA.
| |
Collapse
|
12
|
Zhou K, Litfin T, Solayman M, Zhao H, Zhou Y, Zhan J. High-throughput split-protein profiling by combining transposon mutagenesis and regulated protein-protein interactions with deep sequencing. Int J Biol Macromol 2022; 203:543-552. [PMID: 35120933 DOI: 10.1016/j.ijbiomac.2022.01.173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 01/27/2022] [Accepted: 01/28/2022] [Indexed: 11/05/2022]
Abstract
Splitting a protein at a position may lead to self- or assisted-complementary fragments depending on whether two resulting fragments can reconstitute to maintain the native function spontaneously or require assistance from two interacting molecules. Assisted complementary fragments with high contrast are an important tool for probing biological interactions. However, only a small number of assisted-complementary split-variants have been identified due to manual, labour-intensive optimization of a candidate gene. Here, we introduce a technique for high-throughput split-protein profiling (HiTS) that allows fast identification of self- and assisted complementary positions by transposon mutagenesis, a rapamycin-regulated FRB-FKBP protein interaction pair, and deep sequencing. We test this technique by profiling three antibiotic-resistant genes (fosfomycin-resistant gene, fosA3, erythromycin-resistant gene, ermB, and chloramphenicol-resistant gene, catI). Self- and assisted complementary fragments discovered by the high-throughput technique were subsequently confirmed by low-throughput testing of individual split positions. Thus, the HiTS technique provides a quicker alternative for discovering the proteins with suitable self- and assisted-complementary split positions when combining with a readout such as fluorescence, bioluminescence, cell survival, gene transcription or genome editing.
Collapse
Affiliation(s)
- Kai Zhou
- Institute for Glycomics and School of Information and Communication Technology, Griffith University, Parklands Dr Southport, QLD 4222, Australia; Institute for Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518055, China
| | - Thomas Litfin
- Institute for Glycomics and School of Information and Communication Technology, Griffith University, Parklands Dr Southport, QLD 4222, Australia
| | - Md Solayman
- Institute for Glycomics and School of Information and Communication Technology, Griffith University, Parklands Dr Southport, QLD 4222, Australia
| | - Huijun Zhao
- Centre for Clean Environment and Energy, Griffith University, Gold Coast Campus, Queensland 4222, Australia
| | - Yaoqi Zhou
- Institute for Glycomics and School of Information and Communication Technology, Griffith University, Parklands Dr Southport, QLD 4222, Australia; Institute for Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518055, China.
| | - Jian Zhan
- Institute for Glycomics and School of Information and Communication Technology, Griffith University, Parklands Dr Southport, QLD 4222, Australia; Institute for Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518055, China.
| |
Collapse
|
13
|
Frosi Y, Ng S, Lin YC, Jiang S, Ramlan SR, Lama D, Verma CS, Asial I, Brown CJ. Development of a Novel Peptide Aptamer that Interacts with the eIF4E Capped-mRNA Binding Site using Peptide Epitope Linker Evolution (PELE). RSC Chem Biol 2022; 3:916-930. [PMID: 35866173 PMCID: PMC9257606 DOI: 10.1039/d2cb00099g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 05/13/2022] [Indexed: 11/21/2022] Open
Abstract
Identifying new binding sites and poses that modify biological function are an important step towards drug discovery. We have identified a novel disulphide constrained peptide that interacts with the cap-binding site of eIF4E, an attractive therapeutic target that is commonly overexpressed in many cancers and plays a significant role in initiating a cancer specific protein synthesis program though binding the 5′cap (7′methyl-guanoisine) moiety found on mammalian mRNAs. The use of disulphide constrained peptides to explore intracellular biological targets is limited by their lack of cell permeability and the instability of the disulphide bond in the reducing environment of the cell, loss of which results in abrogation of binding. To overcome these challenges, the cap-binding site interaction motif was placed in a hypervariable loop on an VH domain, and then selections performed to select a molecule that could recapitulate the interaction of the peptide with the target of interest in a process termed Peptide Epitope Linker Evolution (PELE). A novel VH domain was identified that interacted with the eIF4E cap binding site with a nanomolar affinity and that could be intracellularly expressed in mammalian cells. Additionally, it was demonstrated to specifically modulate eIF4E function by decreasing cap-dependent translation and cyclin D1 expression, common effects of eIF4F complex disruption. Identifying new binding sites and poses that modify biological function are an important step towards drug discovery.![]()
Collapse
Affiliation(s)
- Yuri Frosi
- Disease Intervention Technology Lab (DITL), IMCB (ASTAR) 8A Biomedical Grove, #06-04/05, Neuros/Immunos 138648 Singapore
| | - Simon Ng
- Disease Intervention Technology Lab (DITL), IMCB (ASTAR) 8A Biomedical Grove, #06-04/05, Neuros/Immunos 138648 Singapore
| | - Yen-Chu Lin
- Insilico Medicine Taiwan Ltd. Suite 2013, No. 333, Sec.1, Keelung Rd., Xinyi Dist. 110 Taipei Taiwan
| | - Shimin Jiang
- Disease Intervention Technology Lab (DITL), IMCB (ASTAR) 8A Biomedical Grove, #06-04/05, Neuros/Immunos 138648 Singapore
| | - Siti Radhiah Ramlan
- Disease Intervention Technology Lab (DITL), IMCB (ASTAR) 8A Biomedical Grove, #06-04/05, Neuros/Immunos 138648 Singapore
| | - Dilraj Lama
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet Biomedicum Quarter 7B-C Solnavägen 9 17165 Solna Sweden
| | - Chandra S Verma
- Bioinformatics Institute (ASTAR) 30 Biopolis Street, #07-01 Matrix 138671 Singapore
| | - Ignacio Asial
- DotBio, 1 Research Link 117604 Singapore
- Nanyang Technological University, School of Biological Sciences Singapore
| | - Christopher J Brown
- Disease Intervention Technology Lab (DITL), IMCB (ASTAR) 8A Biomedical Grove, #06-04/05, Neuros/Immunos 138648 Singapore
| |
Collapse
|
14
|
Horikawa M, Kakiuchi Y, Kashima D, Ogawa K, Kawahara M. Thrombopoietin receptor-based protein-protein interaction screening (THROPPIS). Biotechnol Bioeng 2021; 119:287-298. [PMID: 34708875 DOI: 10.1002/bit.27975] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 10/20/2021] [Accepted: 10/23/2021] [Indexed: 12/12/2022]
Abstract
As protein-protein interactions (PPIs) are involved in many cellular events, development of mammalian cytosolic PPI detection systems is important for drug discovery as well as understanding biological phenomena. We have previously reported a c-kit-based PPI screening (KIPPIS) system, in which proteins of interest were fused with a receptor tyrosine kinase c-kit, leading to intracellular PPI-dependent cell growth. However, it has not been investigated whether PPI can be detected using other receptors. In this study, we employed a thrombopoietin receptor, which belongs to the Type I cytokine receptor family, to develop a thrombopoietin receptor-based PPI screening (THROPPIS) system. To improve the sensitivity of THROPPIS, we examined two strategies of (i) localization of the chimeric receptors on the cell membrane, and (ii) addition of a helper module to the chimeric receptors. Intriguingly, the nonlocalized chimeric receptor showed the best performance of THROPPIS. Furthermore, the addition of the helper module dramatically improved the detection sensitivity. In total, 5 peptide-domain interactions were detected successfully, demonstrating the versatility of THROPPIS. In addition, a peptide-domain interaction was detected even when insulin receptor or epidermal growth factor receptor was used as a signaling domain, demonstrating that this PPI detection system can be extended to other receptors.
Collapse
Affiliation(s)
- Makiko Horikawa
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Yosuke Kakiuchi
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Daiki Kashima
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Kenichiro Ogawa
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Masahiro Kawahara
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.,Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.,Laboratory of Cell Vaccine, Center for Vaccine and Adjuvant Research (CVAR), National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Ibaraki-shi, Osaka, Japan
| |
Collapse
|
15
|
Kainulainen MH, Bergeron E, Chatterjee P, Chapman AP, Lee J, Chida A, Tang X, Wharton RE, Mercer KB, Petway M, Jenks HM, Flietstra TD, Schuh AJ, Satheshkumar PS, Chaitram JM, Owen SM, McMullan LK, Flint M, Finn MG, Goldstein JM, Montgomery JM, Spiropoulou CF. High-throughput quantitation of SARS-CoV-2 antibodies in a single-dilution homogeneous assay. Sci Rep 2021; 11:12330. [PMID: 34112850 PMCID: PMC8192771 DOI: 10.1038/s41598-021-91300-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 05/18/2021] [Indexed: 12/02/2022] Open
Abstract
SARS-CoV-2 emerged in late 2019 and has since spread around the world, causing a pandemic of the respiratory disease COVID-19. Detecting antibodies against the virus is an essential tool for tracking infections and developing vaccines. Such tests, primarily utilizing the enzyme-linked immunosorbent assay (ELISA) principle, can be either qualitative (reporting positive/negative results) or quantitative (reporting a value representing the quantity of specific antibodies). Quantitation is vital for determining stability or decline of antibody titers in convalescence, efficacy of different vaccination regimens, and detection of asymptomatic infections. Quantitation typically requires two-step ELISA testing, in which samples are first screened in a qualitative assay and positive samples are subsequently analyzed as a dilution series. To overcome the throughput limitations of this approach, we developed a simpler and faster system that is highly automatable and achieves quantitation in a single-dilution screening format with sensitivity and specificity comparable to those of ELISA.
Collapse
Affiliation(s)
- Markus H Kainulainen
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, 1600 Clifton Rd, Atlanta, GA, 30329, USA
| | - Eric Bergeron
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, 1600 Clifton Rd, Atlanta, GA, 30329, USA
| | - Payel Chatterjee
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, 1600 Clifton Rd, Atlanta, GA, 30329, USA
| | - Asheley P Chapman
- School of Chemistry and Biochemistry, School of Biological Sciences, Georgia Institute of Technology, 901 Atlantic Dr., Atlanta, GA, 30332, USA
| | - Joo Lee
- Reagent and Diagnostic Services Branch, Division of Scientific Resources, Centers for Disease Control and Prevention, 1600 Clifton Rd, Atlanta, GA, 30329, USA
| | - Asiya Chida
- Reagent and Diagnostic Services Branch, Division of Scientific Resources, Centers for Disease Control and Prevention, 1600 Clifton Rd, Atlanta, GA, 30329, USA
| | - Xiaoling Tang
- Reagent and Diagnostic Services Branch, Division of Scientific Resources, Centers for Disease Control and Prevention, 1600 Clifton Rd, Atlanta, GA, 30329, USA
| | - Rebekah E Wharton
- Emergency Response Branch, Division of Laboratory Sciences, Centers for Disease Control and Prevention, 4770 Buford Hwy., Atlanta, GA, 30341, USA
| | - Kristina B Mercer
- Newborn Screening and Molecular Biology Branch, Division of Laboratory Sciences, Centers for Disease Control and Prevention, 4770 Buford Hwy., Atlanta, GA, 30341, USA
| | - Marla Petway
- Reagent and Diagnostic Services Branch, Division of Scientific Resources, Centers for Disease Control and Prevention, 1600 Clifton Rd, Atlanta, GA, 30329, USA
| | - Harley M Jenks
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, 1600 Clifton Rd, Atlanta, GA, 30329, USA
| | - Timothy D Flietstra
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, 1600 Clifton Rd, Atlanta, GA, 30329, USA
| | - Amy J Schuh
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, 1600 Clifton Rd, Atlanta, GA, 30329, USA
| | - Panayampalli S Satheshkumar
- Poxvirus and Rabies Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, 1600 Clifton Rd, Atlanta, GA, 30329, USA
| | - Jasmine M Chaitram
- Division of Laboratory Systems, Centers for Disease Control and Prevention, 1600 Clifton Rd, Atlanta, GA, 30329, USA
| | - S Michele Owen
- National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, 1600 Clifton Rd, Atlanta, GA, 30329, USA
| | - Laura K McMullan
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, 1600 Clifton Rd, Atlanta, GA, 30329, USA
| | - Mike Flint
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, 1600 Clifton Rd, Atlanta, GA, 30329, USA
| | - M G Finn
- School of Chemistry and Biochemistry, School of Biological Sciences, Georgia Institute of Technology, 901 Atlantic Dr., Atlanta, GA, 30332, USA
| | - Jason M Goldstein
- Reagent and Diagnostic Services Branch, Division of Scientific Resources, Centers for Disease Control and Prevention, 1600 Clifton Rd, Atlanta, GA, 30329, USA
| | - Joel M Montgomery
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, 1600 Clifton Rd, Atlanta, GA, 30329, USA
| | - Christina F Spiropoulou
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, 1600 Clifton Rd, Atlanta, GA, 30329, USA.
| |
Collapse
|
16
|
Miller CJ, McGinnis JE, Martinez MJ, Wang G, Zhou J, Simmons E, Amet T, Abdeen SJ, Van Huysse JW, Bowsher RR, Kay BK. FN3-based monobodies selective for the receptor binding domain of the SARS-CoV-2 spike protein. N Biotechnol 2021; 62:79-85. [PMID: 33556628 PMCID: PMC7863792 DOI: 10.1016/j.nbt.2021.01.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 01/19/2021] [Accepted: 01/31/2021] [Indexed: 12/17/2022]
Abstract
A phage library displaying 1010 variants of the fibronectin type III (FN3) domain was affinity selected with the biotinylated form of the receptor binding domain (RBD, residues 319-541) of the SARS-CoV-2 virus spike protein. Nine binding FN3 variants (i.e. monobodies) were recovered, representing four different primary structures. Soluble forms of the monobodies bound to several different preparations of the RBD and the S1 spike subunit, with affinities ranging from 3 to 14 nM as measured by bio-layer interferometry. Three of the four monobodies bound selectively to the RBD of SARS-CoV-2, with the fourth monobody showing slight cross-reactivity to the RBD of SARS-CoV-1 virus. Examination of binding to the spike fragments and its trimeric form revealed that the monobodies recognise at least three overlapping epitopes on the RBD of SARS-CoV-2. While pairwise tests failed to identify a monobody pair that could bind simultaneously to the RBD, one monobody could simultaneously bind to the RBD with the ectodomain of the cellular receptor angiotensin converting enzyme 2 (ACE2). All four monobodies successfully bound the RBD after overexpression in Chinese hamster ovary (CHO) cells as fusions to the Fc domain of human IgG1.
Collapse
Affiliation(s)
- Christina J Miller
- Tango Biosciences, Inc., 2201 W. Campbell Park Drive, Chicago, IL 60612 USA
| | | | - Michael J Martinez
- Tango Biosciences, Inc., 2201 W. Campbell Park Drive, Chicago, IL 60612 USA
| | - Guangli Wang
- Euprotein Inc., 675 US Highway 1, Suite 129, North Brunswick, NJ 08902 USA
| | - Jian Zhou
- LifeTein LLC, 100 Randolph Road, Suite 2D, Somerset, NJ 08873 USA
| | - Erica Simmons
- B2S Life Sciences, 97 East Monroe Street, Franklin, IN 46131 USA
| | - Tohti Amet
- B2S Life Sciences, 97 East Monroe Street, Franklin, IN 46131 USA
| | - Sanofar J Abdeen
- B2S Life Sciences, 97 East Monroe Street, Franklin, IN 46131 USA
| | | | - Ronald R Bowsher
- B2S Life Sciences, 97 East Monroe Street, Franklin, IN 46131 USA
| | - Brian K Kay
- Tango Biosciences, Inc., 2201 W. Campbell Park Drive, Chicago, IL 60612 USA.
| |
Collapse
|
17
|
Caminati G, Procacci P. Mounting evidence of FKBP12 implication in neurodegeneration. Neural Regen Res 2020; 15:2195-2202. [PMID: 32594030 PMCID: PMC7749462 DOI: 10.4103/1673-5374.284980] [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: 02/03/2020] [Revised: 02/18/2020] [Accepted: 03/24/2020] [Indexed: 12/25/2022] Open
Abstract
Intrinsically disordered proteins, such as tau or α-synuclein, have long been associated with a dysfunctional role in neurodegenerative diseases. In Alzheimer's and Parkinson's' diseases, these proteins, sharing a common chemical-physical pattern with alternating hydrophobic and hydrophilic domains rich in prolines, abnormally aggregate in tangles in the brain leading to progressive loss of neurons. In this review, we present an overview linking the studies on the implication of the peptidyl-prolyl isomerase domain of immunophilins, and notably FKBP12, to a variety of neurodegenerative diseases, focusing on the molecular origin of such a role. The involvement of FKBP12 dysregulation in the aberrant aggregation of disordered proteins pinpoints this protein as a possible therapeutic target and, at the same time, as a predictive biomarker for early diagnosis in neurodegeneration, calling for the development of reliable, fast and cost-effective detection methods in body fluids for community-based screening campaigns.
Collapse
Affiliation(s)
- Gabriella Caminati
- Department of Chemistry “Ugo Schiff”, University of Florence, Sesto Fiorentino, Italy
- Center for Colloid and Surface Science (CSGI), University of Florence, Sesto Fiorentino, Italy
| | - Piero Procacci
- Department of Chemistry “Ugo Schiff”, University of Florence, Sesto Fiorentino, Italy
| |
Collapse
|
18
|
Lee LY, Pandey AK, Maron BA, Loscalzo J. Network medicine in Cardiovascular Research. Cardiovasc Res 2020; 117:2186-2202. [PMID: 33165538 DOI: 10.1093/cvr/cvaa321] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 09/08/2020] [Accepted: 10/30/2020] [Indexed: 12/21/2022] Open
Abstract
The ability to generate multi-omics data coupled with deeply characterizing the clinical phenotype of individual patients promises to improve understanding of complex cardiovascular pathobiology. There remains an important disconnection between the magnitude and granularity of these data and our ability to improve phenotype-genotype correlations for complex cardiovascular diseases. This shortcoming may be due to limitations associated with traditional reductionist analytical methods, which tend to emphasize a single molecular event in the pathogenesis of diseases more aptly characterized by crosstalk between overlapping molecular pathways. Network medicine is a rapidly growing discipline that considers diseases as the consequences of perturbed interactions between multiple interconnected biological components. This powerful integrative approach has enabled a number of important discoveries in complex disease mechanisms. In this review, we introduce the basic concepts of network medicine and highlight specific examples by which this approach has accelerated cardiovascular research. We also review how network medicine is well-positioned to promote rational drug design for patients with cardiovascular diseases, with particular emphasis on advancing precision medicine.
Collapse
Affiliation(s)
- Laurel Y Lee
- Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, 75 Francis Street, Boston, MA 02115, USA
| | - Arvind K Pandey
- Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, 75 Francis Street, Boston, MA 02115, USA
| | - Bradley A Maron
- Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, 75 Francis Street, Boston, MA 02115, USA.,Department of Cardiology, Boston VA Healthcare System, Boston, MA, USA
| | - Joseph Loscalzo
- Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, 75 Francis Street, Boston, MA 02115, USA
| |
Collapse
|
19
|
Abstract
Bioluminescence (BL) is an excellent optical readout platform that has great potential to be utilized in various bioassays and molecular imaging. The advantages of BL-based bioassays include the long dynamic range, minimal background, high signal-to-noise ratios, biocompatibility for use in cell-based assays, no need of external light source for excitation, simplicity in the measurement system, and versatility in the assay design. The recent intensive research in BL has greatly diversified the available luciferase-luciferin systems in the bioassay toolbox. However, the wide variety does not promise their successful utilization in various bioassays as new tools. This is mainly due to complexity and confusion with the diversity, and the unavailability of defined standards. This review is intended to provide an overview of recent basic developments and applications in BL studies, and showcases the bioanalytical utilities. We hope that this review can be used as an instant reference on BL and provides useful guidance for readers in narrowing down their potential options in their own assay designs.
Collapse
Affiliation(s)
- Sung-Bae Kim
- Research Institute for Environmental Management Technology, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Ramasamy Paulmurugan
- Molecular Imaging Program at Stanford, Bio-X Program, Stanford University School of Medicine
| |
Collapse
|
20
|
Herholt A, Galinski S, Geyer PE, Rossner MJ, Wehr MC. Multiparametric Assays for Accelerating Early Drug Discovery. Trends Pharmacol Sci 2020; 41:318-335. [PMID: 32223968 DOI: 10.1016/j.tips.2020.02.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 02/21/2020] [Accepted: 02/27/2020] [Indexed: 02/07/2023]
Abstract
Drug discovery campaigns are hampered by substantial attrition rates largely due to a lack of efficacy and safety reasons associated with candidate drugs. This is true in particular for genetically complex diseases, where insufficient knowledge of the modulatory actions of candidate drugs on targets and entire target pathways further adds to the problem of attrition. To better profile compound actions on targets, potential off-targets, and disease-linked pathways, new innovative technologies need to be developed that can elucidate the complex cellular signaling networks in health and disease. Here, we discuss progress in genetically encoded multiparametric assays and mass spectrometry (MS)-based proteomics, which both represent promising toolkits to profile multifactorial actions of drug candidates in disease-relevant cellular systems to promote drug discovery and personalized medicine.
Collapse
Affiliation(s)
- Alexander Herholt
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Nussbaumstr. 7, 80336 Munich, Germany; Systasy Bioscience GmbH, Balanstr. 6, 81669, Munich, Germany
| | - Sabrina Galinski
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Nussbaumstr. 7, 80336 Munich, Germany; Systasy Bioscience GmbH, Balanstr. 6, 81669, Munich, Germany
| | - Philipp E Geyer
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Planegg, Germany; NNF Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark; OmicEra Diagnostics GmbH, Am Klopferspitz 19, 82152, Planegg, Germany
| | - Moritz J Rossner
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Nussbaumstr. 7, 80336 Munich, Germany
| | - Michael C Wehr
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Nussbaumstr. 7, 80336 Munich, Germany; Systasy Bioscience GmbH, Balanstr. 6, 81669, Munich, Germany.
| |
Collapse
|
21
|
Moustaqil M, Gambin Y, Sierecki E. Biophysical Techniques for Target Validation and Drug Discovery in Transcription-Targeted Therapy. Int J Mol Sci 2020; 21:E2301. [PMID: 32225120 PMCID: PMC7178067 DOI: 10.3390/ijms21072301] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 03/13/2020] [Accepted: 03/13/2020] [Indexed: 01/10/2023] Open
Abstract
In the post-genome era, pathologies become associated with specific gene expression profiles and defined molecular lesions can be identified. The traditional therapeutic strategy is to block the identified aberrant biochemical activity. However, an attractive alternative could aim at antagonizing key transcriptional events underlying the pathogenesis, thereby blocking the consequences of a disorder, irrespective of the original biochemical nature. This approach, called transcription therapy, is now rendered possible by major advances in biophysical technologies. In the last two decades, techniques have evolved to become key components of drug discovery platforms, within pharmaceutical companies as well as academic laboratories. This review outlines the current biophysical strategies for transcription manipulation and provides examples of successful applications. It also provides insights into the future development of biophysical methods in drug discovery and personalized medicine.
Collapse
Affiliation(s)
- Mehdi Moustaqil
- EMBL Australia Node in Single Molecule Science and School of Medical Sciences, UNSW Sydney, NSW 2052, Australia;
| | | | - Emma Sierecki
- EMBL Australia Node in Single Molecule Science and School of Medical Sciences, UNSW Sydney, NSW 2052, Australia;
| |
Collapse
|
22
|
PeSA: A software tool for peptide specificity analysis. Comput Biol Chem 2019; 83:107145. [DOI: 10.1016/j.compbiolchem.2019.107145] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 09/17/2019] [Accepted: 10/08/2019] [Indexed: 12/11/2022]
|