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Wu Y, Liu B, Liu Z, Zhang P, Mu X, Tong Z. Construction, Characterization, and Application of a Nonpathogenic Virus-like Model for SARS-CoV-2 Nucleocapsid Protein by Phage Display. Toxins (Basel) 2022; 14:toxins14100683. [PMID: 36287952 PMCID: PMC9607219 DOI: 10.3390/toxins14100683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/29/2022] [Accepted: 09/30/2022] [Indexed: 11/07/2022] Open
Abstract
With the outbreak and spread of COVID-19, a deep investigation of SARS-CoV-2 is urgent. Direct usage of this virus for scientific research could provide reliable results and authenticity. However, it is strictly constrained and unrealistic due to its high pathogenicity and infectiousness. Considering its biosafety, different systems and technologies have been employed in immunology and biomedical studies. In this study, phage display technology was used to construct a nonpathogenic model for COVID-19 research. The nucleocapsid protein of SARS-CoV-2 was fused with the M13 phage capsid p3 protein and expressed on the M13 phages. After validation of its successful expression, its potential as the standard for qPCR quantification and affinity with antibodies were confirmed, which may show the possibility of using this nonpathogenic bacteriophage to replace the pathogenic virus in scientific research concerning SARS-CoV-2. In addition, the model was used to develop a system for the classification and identification of different samples using ATR–FTIR, which may provide an idea for the development and evaluation of virus monitoring equipment in the future.
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Dau PT, Ishibashi H, Tuyen LH, Sakai H, Hirano M, Kim EY, Iwata H. Assessment of binding potencies of polychlorinated biphenyls and polybrominated diphenyl ethers with Baikal seal and mouse constitutive androstane receptors: Comparisons across species and congeners. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 806:150631. [PMID: 34592282 DOI: 10.1016/j.scitotenv.2021.150631] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 09/23/2021] [Accepted: 09/23/2021] [Indexed: 06/13/2023]
Abstract
The present study evaluated the binding potencies (equilibrium dissociation constant: KD) of polychlorinated biphenyls (PCBs) and polybrominated diphenyl ethers (PBDEs) with the constitutive androstane receptor (CAR)_ligand binding domain (LBD) of the Baikal seal (bsCAR_LBD) and mouse (mCAR_LBD) using a surface plasmon resonance (SPR) biosensor. The binding affinities of individual congeners with mCAR_LBD tended to be higher than those with bsCAR_LBD but the differences were within the same order of magnitude. Notably, PBDE congeners showed higher binding affinities for both CAR_LBDs than PCB congeners. In silico docking simulations demonstrated that PBDEs had more non-covalent interactions with specific amino acid residues in both CAR_LBDs than PCBs, supporting the results of their binding affinities. Binding affinity comparisons among congeners revealed the structural requirements for higher binding; mono or di ortho-, tri meta-, and di para‑chlorine substitutions for PCBs, and di or tri ortho-, mono meta-, and di para‑bromine substitutions for PBDEs. The binding potencies of these congeners unlikely accounted for their previously reported CAR-mediated transactivation potencies, implying that their transactivation is regulated in a ligand-dependent, but a distinct manner from ligand binding. Risk assessment analysis showed that the KD values of individual PCB and PBDE congeners were 1-4 orders of magnitude higher than their respective hepatic concentrations in wild Baikal seal population.
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Affiliation(s)
- Pham Thi Dau
- Centre for Life Science Research, Faculty of Biology, VNU University of Science, 334 Nguyen Trai, Hanoi, Viet Nam.
| | - Hiroshi Ishibashi
- Graduate School of Agriculture, Ehime University, Matsuyama 790-8566, Japan
| | - Le Huu Tuyen
- Research Centre for Environmental Technology and Sustainable Development, VNU University of Science, 334 Nguyen Trai, Hanoi, Viet Nam
| | - Hiroki Sakai
- Division of Pharmacology, Yamaguchi University Graduate School of Medicine, Yamaguchi 755-8505, Japan
| | - Masashi Hirano
- Department of Bioscience, School of Agriculture, Tokai University, 9-1-1 Toroku, Higashi-ku, Kumamoto-shi, Kumamoto 862-8652, Japan
| | - Eun-Young Kim
- Department of Life and Nanopharmaceutical Science and Department of Biology, Kyung Hee University, Hoegi-Dong, Dongdaemun-Gu, Seoul 130-701, Republic of Korea
| | - Hisato Iwata
- Center for Marine Environmental Studies (CMES), Ehime University, Matsuyama 790-8577, Japan.
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Lubken RM, Bergkamp MH, de Jong AM, Prins MWJ. Sensing Methodology for the Rapid Monitoring of Biomolecules at Low Concentrations over Long Time Spans. ACS Sens 2021; 6:4471-4481. [PMID: 34854303 PMCID: PMC8715529 DOI: 10.1021/acssensors.1c01991] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
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Studies on the dynamics
of biological systems and biotechnological
processes require measurement techniques that can reveal time dependencies
of concentrations of specific biomolecules, preferably with small
time delays, short time intervals between subsequent measurements,
and the possibility to record over long time spans. For low-concentration
biomolecules, these requirements are very challenging since low-concentration
assays are typically slow and require new reagents in every assay.
Here, we present a sensing methodology that enables rapid monitoring
of picomolar and sub-picomolar concentrations in a reversible affinity-based
assay, studied using simulations. We demonstrate that low-concentration
biomolecules can be monitored with small time delays, short time intervals,
and in principle over an endless time span.
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Affiliation(s)
- Rafiq M. Lubken
- Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven 5612 AZ, The Netherlands
- Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Eindhoven 5612 AZ, The Netherlands
| | - Max H. Bergkamp
- Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven 5612 AZ, The Netherlands
- Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Eindhoven 5612 AZ, The Netherlands
| | - Arthur M. de Jong
- Department of Applied Physics, Eindhoven University of Technology, Eindhoven 5612 AZ, The Netherlands
- Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Eindhoven 5612 AZ, The Netherlands
| | - Menno W. J. Prins
- Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven 5612 AZ, The Netherlands
- Department of Applied Physics, Eindhoven University of Technology, Eindhoven 5612 AZ, The Netherlands
- Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Eindhoven 5612 AZ, The Netherlands
- Helia Biomonitoring, Eindhoven 5612 AZ, The Netherlands
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Shen Y, Li YM, Zhou JJ, Zhou Z, Xu YC, Zhao WB, Chen SQ. The Antitumor Activity of TCR-Mimic Antibody-Drug Conjugates (TCRm-ADCs) Targeting the Intracellular Wilms Tumor 1 (WT1) Oncoprotein. Int J Mol Sci 2019; 20:ijms20163912. [PMID: 31408937 PMCID: PMC6720711 DOI: 10.3390/ijms20163912] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 08/02/2019] [Accepted: 08/08/2019] [Indexed: 01/13/2023] Open
Abstract
Wilms tumor 1 (WT1) oncoprotein is an intracellular oncogenic transcription factor which is barely expressed in normal adult tissues but over expressed in a variety of leukemias and solid cancers. WT1-derived HLA-A*02:01 T cell epitope, RMFPNAPYL (RMF), is a validated target for T cell-based immunotherapy. We generated two T cell receptor mimic antibody-drug conjugates (TCRm-ADCs), ESK-MMAE, and Q2L-MMAE, against WT1 RMF/HLA-A*02:01 complex with distinct affinities, which mediate specific antitumor activity. Although ESK-MMAE showed higher tumor growth inhibition ratio in vivo, the efficacy of them was not so promising, which might be due to low expression of peptide/HLA targets. Therefore, we explored a bispecific TCRm-ADC that exerted more potent tumor cytotoxicity compared with TCRm-ADCs. Hence, our findings validate the feasibility of the presenting intracellular peptides as the targets of ADCs, which broadens the antigen selection range of antibody-based drugs and provides new strategies for precision medicine in tumor therapy.
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Affiliation(s)
- Ying Shen
- Laboratory of Precision Medicine and Biopharmaceutics & Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yi-Ming Li
- Laboratory of Precision Medicine and Biopharmaceutics & Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jing-Jing Zhou
- Laboratory of Precision Medicine and Biopharmaceutics & Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Zhan Zhou
- Laboratory of Precision Medicine and Biopharmaceutics & Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Ying-Chun Xu
- Laboratory of Precision Medicine and Biopharmaceutics & Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Wen-Bin Zhao
- Laboratory of Precision Medicine and Biopharmaceutics & Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Shu-Qing Chen
- Laboratory of Precision Medicine and Biopharmaceutics & Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.
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Yang D, Singh A, Wu H, Kroe-Barrett R. Determination of High-affinity Antibody-antigen Binding Kinetics Using Four Biosensor Platforms. J Vis Exp 2017. [PMID: 28448040 PMCID: PMC5564993 DOI: 10.3791/55659] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Label-free optical biosensors are powerful tools in drug discovery for the characterization of biomolecular interactions. In this study, we describe the use of four routinely used biosensor platforms in our laboratory to evaluate the binding affinity and kinetics of ten high-affinity monoclonal antibodies (mAbs) against human proprotein convertase subtilisin kexin type 9 (PCSK9). While both Biacore T100 and ProteOn XPR36 are derived from the well-established Surface Plasmon Resonance (SPR) technology, the former has four flow cells connected by serial flow configuration, whereas the latter presents 36 reaction spots in parallel through an improvised 6 x 6 crisscross microfluidic channel configuration. The IBIS MX96 also operates based on the SPR sensor technology, with an additional imaging feature that provides detection in spatial orientation. This detection technique coupled with the Continuous Flow Microspotter (CFM) expands the throughput significantly by enabling multiplex array printing and detection of 96 reaction sports simultaneously. In contrast, the Octet RED384 is based on the BioLayer Interferometry (BLI) optical principle, with fiber-optic probes acting as the biosensor to detect interference pattern changes upon binding interactions at the tip surface. Unlike the SPR-based platforms, the BLI system does not rely on continuous flow fluidics; instead, the sensor tips collect readings while they are immersed in analyte solutions of a 384-well microplate during orbital agitation. Each of these biosensor platforms has its own advantages and disadvantages. To provide a direct comparison of these instruments' ability to provide quality kinetic data, the described protocols illustrate experiments that use the same assay format and the same high-quality reagents to characterize antibody-antigen kinetics that fit the simple 1:1 molecular interaction model.
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Affiliation(s)
- Danlin Yang
- Department of Biotherapeutics Discovery, Immune Modulation and Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceuticals, Inc
| | - Ajit Singh
- The Fu Foundation School of Engineering and Applied Science, Columbia University
| | - Helen Wu
- Department of Biotherapeutics Discovery, Immune Modulation and Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceuticals, Inc
| | - Rachel Kroe-Barrett
- Department of Biotherapeutics Discovery, Immune Modulation and Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceuticals, Inc.;
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