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Wilford T, Bartlett PD, Schlag A, Jasaitis L, Pandha H, Pierce AJ, Hughes R. Solving selectivity issues in LBAs: case study using Gyrolab to quantify CB307, a bispecific Humabody in human serum. Bioanalysis 2024:1-13. [PMID: 38957926 DOI: 10.1080/17576180.2024.2365545] [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: 02/15/2024] [Accepted: 06/05/2024] [Indexed: 07/04/2024] Open
Abstract
Aim: Endogenous interferents can cause nonselectivity in ligand binding pharmacokinetic assays, leading to inaccurate quantification of drug concentrations. We describe the development of a Gyrolab immunoassay to quantify a new modality, CB307 and discuss strategies implemented to overcome matrix effects and achieve selectivity at the desired sensitivity. Results: Matrix effects were mitigated using strategies including increasing minimum required dilution (MRD) and lower limit of quantification, optimization of antibody orientation, assay buffer and solid phase. Conclusion: The strategies described resulted in a selective method for CB307 in disease state matrix that met bioanalytical method validation (BMV) guidance and is currently used to support clinical pharmacokinetic sample analysis in the first-in-human POTENTIA clinical study (NCT04839991) as a secondary clinical end point.
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Affiliation(s)
- Thomas Wilford
- Resolian, Fordham, Cambridgeshire CB7 5WW, United Kingdom of Great Britain & Northern Ireland
| | - Phillip D Bartlett
- Crescendo Biologics Limited, Cambridge CB22 3AT, United Kingdom of Great Britain & Northern Ireland
| | - Anna Schlag
- Crescendo Biologics Limited, Cambridge CB22 3AT, United Kingdom of Great Britain & Northern Ireland
| | - Lukas Jasaitis
- Crescendo Biologics Limited, Cambridge CB22 3AT, United Kingdom of Great Britain & Northern Ireland
| | - Hardev Pandha
- University of Surrey, School of Biosciences, Guildford GU2 7XH, Surrey, United Kingdom of Great Britain & Northern Ireland
| | - Andrew J Pierce
- Crescendo Biologics Limited, Cambridge CB22 3AT, United Kingdom of Great Britain & Northern Ireland
| | - Richard Hughes
- Resolian, Fordham, Cambridgeshire CB7 5WW, United Kingdom of Great Britain & Northern Ireland
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2
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Agu CV, Cook RL, Martelly W, Gushgari LR, Mohan M, Takulapalli B. Novel sensor-integrated proteome on chip (SPOC) platform with thousands of folded proteins on a 1.5 sq-cm biosensor chip to enable high-throughput real-time label-free screening for kinetic analysis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.23.575909. [PMID: 38328216 PMCID: PMC10849568 DOI: 10.1101/2024.01.23.575909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
An automated proteomic platform for producing and screening an array of functional proteins on biosensor surfaces was developed to address the challenges of measuring proteomic interaction kinetics in high throughput (HTP). This technology is termed Sensor-Integrated Proteome On Chip (SPOC®) which involves in-situ cell-free protein expression in nano-liter volume wells (nanowells) directly from rapidly customizable arrays of plasmid DNA, facilitating simultaneous capture-purification of up to 2400 unique full-length folded proteins onto a 1.5 sq-cm surface of a single gold biosensor chip. Arrayed SPOC sensors can then be screened by real-time label-free analysis, including surface plasmon resonance (SPR) to generate kinetic affinity, avidity data. Fluorescent and SPR assays were used to demonstrate zero crosstalk between protein spots. The functionality of the SPOC protein array was validated by antibody binding assay, post-translational modification, mutation-mediated differential binding kinetics, and catalytic activity screening on model SPOC protein arrays containing p53, Src, Jun, Fos, HIST1H3A, and SARS-CoV-2 receptor binding domain (RBD) protein variants of interest, among others. Monoclonal antibodies were found to selectively bind their target proteins on the SPOC array. A commercial anti-RBD antibody was used to demonstrate discriminatory binding to numerous SARS-CoV-2 RBD variants of concern with comprehensive kinetic information. With advantages of HTP, flexibility, low-cost, quick turnaround time, and real-time kinetic affinity profiling, the SPOC proteomic platform addresses the challenges of interrogating protein interactions at scale and can be deployed in various research and clinical applications.
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Affiliation(s)
- Chidozie Victor Agu
- SPOC Proteomics, Inc. 7201 E Henkel Way Suite 285, Scottsdale AZ 85255, United States
| | - Rebecca L Cook
- SPOC Proteomics, Inc. 7201 E Henkel Way Suite 285, Scottsdale AZ 85255, United States
| | - William Martelly
- SPOC Proteomics, Inc. 7201 E Henkel Way Suite 285, Scottsdale AZ 85255, United States
| | - Lydia R Gushgari
- SPOC Proteomics, Inc. 7201 E Henkel Way Suite 285, Scottsdale AZ 85255, United States
| | - Mukilan Mohan
- SPOC Proteomics, Inc. 7201 E Henkel Way Suite 285, Scottsdale AZ 85255, United States
| | - Bharath Takulapalli
- SPOC Proteomics, Inc. 7201 E Henkel Way Suite 285, Scottsdale AZ 85255, United States
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3
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Janezic EM, Doan A, Mai E, Bravo DD, Wang J, Kim HS, Spiess C, Bewley K, ElSohly A, Liang WC, Koerber JT, Richalet P, Vanhove M, Comps-Agrar L. A novel, label-free, pre-equilibrium assay to determine the association and dissociation rate constants of therapeutic antibodies on living cells. Br J Pharmacol 2023. [PMID: 37783572 DOI: 10.1111/bph.16258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 09/19/2023] [Accepted: 09/23/2023] [Indexed: 10/04/2023] Open
Abstract
BACKGROUND AND PURPOSE Monoclonal antibodies (Ab) represent the fastest growing drug class. Knowledge of the biophysical parameters (kon , koff and KD ) that dictate Ab:receptor interaction is critical during the drug discovery process. However, with the increasing complexity of Ab formats and their targets, it became apparent that existing technologies present limitations and are not always suitable to determine these parameters. Therefore, novel affinity determination methods represent an unmet assay need. EXPERIMENTAL APPROACH We developed a pre-equilibrium kinetic exclusion assay using recent mathematical advances to determine the kon , koff and KD of monoclonal Ab:receptor interactions on living cells. The assay is amenable to all human IgG1 and rabbit Abs. KEY RESULTS Using our novel assay, we demonstrated for several monoclonal Ab:receptor pairs that the calculated kinetic rate constants were comparable with orthogonal methods that were lower throughput or more resource consuming. We ran simulations to predict the critical conditions to improve the performance of the assays. We further showed that this method could successfully be applied to both suspension and adherent cells. Finally, we demonstrated that kon and koff , but not KD , correlate with in vitro potency for a panel of monoclonal Abs. CONCLUSIONS AND IMPLICATIONS Our novel assay has the potential to systematically probe binding kinetics of monoclonal Abs to cells and can be incorporated in a screening cascade to identify new therapeutic candidates. Wide-spread adoption of pre-equilibrium assays using physiologically relevant systems will lead to a more holistic understanding of how Ab binding kinetics influence their potency.
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Affiliation(s)
| | | | - Elaine Mai
- Genentech, Inc, South San Francisco, California, USA
| | | | - Jianyong Wang
- Genentech, Inc, South San Francisco, California, USA
| | - Hok Seon Kim
- Genentech, Inc, South San Francisco, California, USA
| | | | | | - Adel ElSohly
- Genentech, Inc, South San Francisco, California, USA
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4
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Truong PL, Yin Y, Lee D, Ko SH. Advancement in COVID-19 detection using nanomaterial-based biosensors. EXPLORATION (BEIJING, CHINA) 2023; 3:20210232. [PMID: 37323622 PMCID: PMC10191025 DOI: 10.1002/exp.20210232] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 05/11/2022] [Indexed: 06/17/2023]
Abstract
Coronavirus disease 2019 (COVID-19) pandemic has exemplified how viral growth and transmission are a significant threat to global biosecurity. The early detection and treatment of viral infections is the top priority to prevent fresh waves and control the pandemic. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been identified through several conventional molecular methodologies that are time-consuming and require high-skill labor, apparatus, and biochemical reagents but have a low detection accuracy. These bottlenecks hamper conventional methods from resolving the COVID-19 emergency. However, interdisciplinary advances in nanomaterials and biotechnology, such as nanomaterials-based biosensors, have opened new avenues for rapid and ultrasensitive detection of pathogens in the field of healthcare. Many updated nanomaterials-based biosensors, namely electrochemical, field-effect transistor, plasmonic, and colorimetric biosensors, employ nucleic acid and antigen-antibody interactions for SARS-CoV-2 detection in a highly efficient, reliable, sensitive, and rapid manner. This systematic review summarizes the mechanisms and characteristics of nanomaterials-based biosensors for SARS-CoV-2 detection. Moreover, continuing challenges and emerging trends in biosensor development are also discussed.
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Affiliation(s)
- Phuoc Loc Truong
- Laser and Thermal Engineering LabDepartment of Mechanical EngineeringGachon UniversitySeongnamKorea
| | - Yiming Yin
- New Materials InstituteDepartment of MechanicalMaterials and Manufacturing EngineeringUniversity of Nottingham Ningbo ChinaNingboChina
- Applied Nano and Thermal Science LabDepartment of Mechanical EngineeringSeoul National UniversityGwanak‐guSeoulKorea
| | - Daeho Lee
- Laser and Thermal Engineering LabDepartment of Mechanical EngineeringGachon UniversitySeongnamKorea
| | - Seung Hwan Ko
- Applied Nano and Thermal Science LabDepartment of Mechanical EngineeringSeoul National UniversityGwanak‐guSeoulKorea
- Institute of Advanced Machinery and Design (SNU‐IAMD)/Institute of Engineering ResearchSeoul National UniversityGwanak‐guSeoulKorea
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5
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Narvekar A, Puranik A, Kulkarni B, Jagtap D, Jain R, Dandekar P. FcγRIIIA affinity chromatography complements conventional functional characterization of rituximab. Biotechnol Prog 2023; 39:e3304. [PMID: 36181372 DOI: 10.1002/btpr.3304] [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: 07/30/2022] [Revised: 09/26/2022] [Accepted: 09/29/2022] [Indexed: 11/06/2022]
Abstract
Analytical and functional characterization of batches of biologics/biosimilar products are imperative towards qualifying them for pre-clinical and clinical investigations. Several orthogonal strategies are employed to characterize the functional attributes of these drugs. However, the use of conventional techniques for online monitoring of functional attributes is not feasible. Liquid chromatography is one of the crucial unit operations during the downstream processing of biopharmaceuticals. In this work, we have demonstrated the utility of FcγRIIIA affinity chromatography as an independent quantitative functional characterization tool. FcγRIIIA affinity chromatography aided in sequential elution of Rituximab glycoform mixtures, based on varying levels of galactosylation, and thereby the affinity for the receptor protein. The predominant glycans present in the three Rituximab glycoform mixture peaks were G0F, G1F, and G2F, respectively. Dissociation rate constants were derived from the chromatographic elution profiles by the peak profiling method, for the control and glucose stress conditions. The glucose stress conditions did not result in unfavorable binding kinetics of Rituximab and FcγRIIIA. The dissociation rate constants of the glycoform mixture 2, predominantly consisting of G1F, were similar to the dissociation rate constants obtained by surface plasmon resonance. Moreover, the glycosylation profiles obtained from chromatographic estimation can be corroborated with the ADCC activity. However, the ex vivo ADCC reporter assay indicated that there was an increase in the effector activity with increasing glucose stress. Thus, FcγRIIIA affinity chromatography permitted three independent assessments via a single analysis. Such approaches can be utilized as potential process analytical technology (PAT) tools in the biosimilar development process.
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Affiliation(s)
- Aditya Narvekar
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Mumbai, India
| | - Amita Puranik
- Department of Chemical Engineering, Institute of Chemical Technology, Mumbai, India
| | - Bhalchandra Kulkarni
- Division of Structural Biology, National Institute for Research in Reproductive and Child Health, Mumbai, India
| | - Dhanashree Jagtap
- Division of Structural Biology, National Institute for Research in Reproductive and Child Health, Mumbai, India
| | - Ratnesh Jain
- Department of Chemical Engineering, Institute of Chemical Technology, Mumbai, India
| | - Prajakta Dandekar
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Mumbai, India
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6
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Gurel B, Berksoz M, Capkin E, Parlar A, Pala MC, Ozkan A, Capan Y, Daglikoca DE, Yuce M. Structural and Functional Analysis of CEX Fractions Collected from a Novel Avastin® Biosimilar Candidate and Its Innovator: A Comparative Study. Pharmaceutics 2022; 14:pharmaceutics14081571. [PMID: 36015197 PMCID: PMC9415858 DOI: 10.3390/pharmaceutics14081571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 07/25/2022] [Accepted: 07/25/2022] [Indexed: 02/01/2023] Open
Abstract
Avastin® is a humanized recombinant monoclonal antibody used to treat cancer by targeting VEGF-A to inhibit angiogenesis. SIMAB054, an Avastin® biosimilar candidate developed in this study, showed a different charge variant profile than its innovator. Thus, it is fractionated into acidic, main, and basic isoforms and collected physically by Cation Exchange Chromatography (CEX) for a comprehensive structural and functional analysis. The innovator product, fractionated into the same species and collected by the same method, is used as a reference for comparative analysis. Ultra-Performance Liquid Chromatography (UPLC) ESI-QToF was used to analyze the modifications leading to charge heterogeneities at intact protein and peptide levels. The C-terminal lysine clipping and glycosylation profiles of the samples were monitored by intact mAb analysis. The post-translational modifications, including oxidation, deamidation, and N-terminal pyroglutamic acid formation, were determined by peptide mapping analysis in the selected signal peptides. The relative binding affinities of the fractionated charge isoforms against the antigen, VEGF-A, and the neonatal receptor, FcRn, were revealed by Surface Plasmon Resonance (SPR) studies. The results show that all CEX fractions from the innovator product and the SIMAB054 shared the same structural variants, albeit in different ratios. Common glycoforms and post-translational modifications were the same, but at different percentages for some samples. The dissimilarities were mostly originating from the presence of extra C-term Lysin residues, which are prone to enzymatic degradation in the body, and thus they were previously assessed as clinically irrelevant. Another critical finding was the presence of different glyco proteoforms in different charge species, such as increased galactosylation in the acidic and afucosylation in the basic species. SPR characterization of the isolated charge variants further confirmed that basic species found in the CEX analyses of the biosimilar candidate were also present in the innovator product, although at lower amounts. The charge variants’ in vitro antigen- and neonatal receptor-binding activities varied amongst the samples, which could be further investigated in vivo with a larger sample set to reveal the impact on the pharmacokinetics of drug candidates. Minor structural differences may explain antigen-binding differences in the isolated charge variants, which is a key parameter in a comparability exercise. Consequently, such a biosimilar candidate may not comply with high regulatory standards unless the binding differences observed are justified and demonstrated not to have any clinical impact.
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Affiliation(s)
- Busra Gurel
- SUNUM Nanotechnology Research and Application Center, Sabanci University, Istanbul 34956, Turkey;
| | - Melike Berksoz
- ILKO ARGEM Biotechnology R&D Center, Istanbul 34906, Turkey; (M.B.); (E.C.); (M.C.P.); (A.O.); (Y.C.)
| | - Eda Capkin
- ILKO ARGEM Biotechnology R&D Center, Istanbul 34906, Turkey; (M.B.); (E.C.); (M.C.P.); (A.O.); (Y.C.)
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul 34956, Turkey;
| | - Ayhan Parlar
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul 34956, Turkey;
| | - Meltem Corbacioglu Pala
- ILKO ARGEM Biotechnology R&D Center, Istanbul 34906, Turkey; (M.B.); (E.C.); (M.C.P.); (A.O.); (Y.C.)
| | - Aylin Ozkan
- ILKO ARGEM Biotechnology R&D Center, Istanbul 34906, Turkey; (M.B.); (E.C.); (M.C.P.); (A.O.); (Y.C.)
| | - Yılmaz Capan
- ILKO ARGEM Biotechnology R&D Center, Istanbul 34906, Turkey; (M.B.); (E.C.); (M.C.P.); (A.O.); (Y.C.)
| | - Duygu Emine Daglikoca
- ILKO ARGEM Biotechnology R&D Center, Istanbul 34906, Turkey; (M.B.); (E.C.); (M.C.P.); (A.O.); (Y.C.)
- Correspondence: (D.E.D.); (M.Y.)
| | - Meral Yuce
- SUNUM Nanotechnology Research and Application Center, Sabanci University, Istanbul 34956, Turkey;
- Correspondence: (D.E.D.); (M.Y.)
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Optimized Methods for Analytical and Functional Comparison of Biosimilar mAb Drugs: A Case Study for Avastin, Mvasi, and Zirabev. Sci Pharm 2022. [DOI: 10.3390/scipharm90020036] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Bevacizumab is a humanized therapeutic monoclonal antibody used to reduce angiogenesis, a hallmark of cancer, by binding to VEGF-A. Many pharmaceutical companies have developed biosimilars of Bevacizumab in the last decade. The official reports provided by the FDA and EMA summarize the analytical performance of biosimilars as compared to the originators without giving detailed analytical procedures. In the current study, several key methods were optimized and reported for analytical and functional comparison of bevacizumab originators (Avastin, Altuzan) and approved commercial biosimilars (Zirabev and Mvasi). This case study presents a comparative analysis of a set of biosimilars under optimized analytical conditions for the first time in the literature. The chemical structure of all products was analyzed at intact protein and peptide levels by high-resolution mass spectrometry; the major glycoforms and posttranslational modifications, including oxidation, deamidation, N-terminal PyroGlu addition, and C-terminal Lys clipping, were compared. The SPR technique was used to reveal antigen and some receptor binding kinetics of all products, and the ELISA technique was used for C1q binding affinity analysis. Finally, the inhibition performance of the samples was evaluated by an MTS-based proliferation assay in vitro. Major glycoforms were similar, with minor differences among the samples. Posttranslational modifications, except C-terminal Lys, were determined similarly, while unclipped Lys percentage was higher in Zirabev. The binding kinetics for VEGF, FcRn, FcγRIa, and C1q were similar or in the value range of originators. The anti-proliferative effect of Zirabev was slightly higher than the originators and Mvasi. The analysis of biosimilars under the same conditions could provide a new aspect to the literature in terms of the applied analytical techniques. Further studies in this field would be helpful to better understand the inter-comparability of the biosimilars.
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8
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Budroni S, Buricchi F, Cavallone A, Volpini G, Mariani A, Lo Surdo P, Blohmke CJ, Del Giudice G, Medini D, Finco O. Computational modeling of microfluidic data provides high-throughput affinity estimates for monoclonal antibodies. Comput Struct Biotechnol J 2021; 19:3664-3672. [PMID: 34257845 PMCID: PMC8255181 DOI: 10.1016/j.csbj.2021.06.024] [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: 12/02/2020] [Revised: 06/14/2021] [Accepted: 06/15/2021] [Indexed: 10/27/2022] Open
Abstract
Affinity measurement is a fundamental step in the discovery of monoclonal antibodies (mAbs) and of antigens suitable for vaccine development. Innovative affinity assays are needed due to the low throughput and/or limited dynamic range of available technologies. We combined microfluidic technology with quantum-mechanical scattering theory, in order to develop a high-throughput, broad-range methodology to measure affinity. Fluorescence intensity profiles were generated for out-of-equilibrium solutions of labelled mAbs and their antigen-binding fragments migrating along micro-columns with immobilized cognate antigen. Affinity quantification was performed by computational data analysis based on the Landau probability distribution. Experiments using a wide array of human or murine antibodies against bacterial or viral, protein or polysaccharide antigens, showed that all the antibody-antigen capture profiles (n = 841) generated at different concentrations were accurately described by the Landau distribution. A scale parameter W, proportional to the full-width-at-half-maximum of the capture profile, was shown to be independent of the antibody concentration. The W parameter correlated significantly (Pearson's r [p-value]: 0.89 [3 × 10-8]) with the equilibrium dissociation constant KD, a gold-standard affinity measure. Our method showed good intermediate precision (median coefficient of variation: 5%) and a dynamic range corresponding to KD values spanning from ~10-7 to ~10-11 Molar. Relative to assays relying on antibody-antigen equilibrium in solution, even when they are microfluidic-based, the method's turnaround times were decreased from 2 days to 2 h. The described computational modelling of antibody capture profiles represents a fast, reproducible, high-throughput methodology to accurately measure a broad range of antibody affinities in very low volumes of solution.
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9
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Bragina VA, Orlov AV, Znoyko SL, Pushkarev AV, Novichikhin DO, Guteneva NV, Nikitin MP, Gorshkov BG, Nikitin PI. Nanobiosensing based on optically selected antibodies and superparamagnetic labels for rapid and highly sensitive quantification of polyvalent hepatitis B surface antigen. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2021; 13:2424-2433. [PMID: 33998615 DOI: 10.1039/d1ay00354b] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Hepatitis B surface antigen (HBsAg) is the most clinically relevant serological marker of hepatitis B virus (HBV) infection. Its detection in blood is extremely important for identification of asymptomatic individuals or chronic HBV carriers, screening blood donors, and early seroconversion. Rapid point-of-care HBsAg tests are predominantly qualitative, and their analytical sensitivity does not meet the requirements of regulatory agencies. We present a highly sensitive lateral flow assay based on superparamagnetic nanoparticles for rapid quantification (within 30 min) of polyvalent HBsAg in serum. The demonstrated limit of detection (LOD) of 80 pg mL-1 in human serum is better than both the FDA recommendations for HBsAg assays (which is 0.5 ng mL-1) and the sensitivity of traditional laboratory-based methods such as enzyme linked immunosorbent assays. Along with the attractive LOD at lower concentrations and the wide linear dynamic range of more than 2.5 orders, the assay features rapidity, user-friendliness, on-site operation and effective performance in the complex biological medium. These are due to the combination of the immunochromatographic approach with a highly sensitive electronic registration of superparamagnetic nanolabels over the entire volume of a 3D test structure by their non-linear magnetization and selection of optimal antibodies by original optical label-free methods. The developed cost-efficient bioanalytical technology can be used in many socially important fields such as out-of-lab screening and diagnosis of HBV infection at a point-of-demand, especially in hard-to-reach or sparsely populated areas, as well as highly endemic regions.
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Affiliation(s)
- Vera A Bragina
- Prokhorov General Physics Institute of the Russian Academy of Sciences, 38 Vavilov St, Moscow, 119991, Russia.
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10
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Carzaniga T, Zanchetta G, Frezza E, Casiraghi L, Vanjur L, Nava G, Tagliabue G, Dieci G, Buscaglia M, Bellini T. A Bit Stickier, a Bit Slower, a Lot Stiffer: Specific vs. Nonspecific Binding of Gal4 to DNA. Int J Mol Sci 2021; 22:ijms22083813. [PMID: 33916983 PMCID: PMC8067546 DOI: 10.3390/ijms22083813] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 03/26/2021] [Accepted: 04/02/2021] [Indexed: 12/15/2022] Open
Abstract
Transcription factors regulate gene activity by binding specific regions of genomic DNA thanks to a subtle interplay of specific and nonspecific interactions that is challenging to quantify. Here, we exploit Reflective Phantom Interface (RPI), a label-free biosensor based on optical reflectivity, to investigate the binding of the N-terminal domain of Gal4, a well-known gene regulator, to double-stranded DNA fragments containing or not its consensus sequence. The analysis of RPI-binding curves provides interaction strength and kinetics and their dependence on temperature and ionic strength. We found that the binding of Gal4 to its cognate site is stronger, as expected, but also markedly slower. We performed a combined analysis of specific and nonspecific binding—equilibrium and kinetics—by means of a simple model based on nested potential wells and found that the free energy gap between specific and nonspecific binding is of the order of one kcal/mol only. We investigated the origin of such a small value by performing all-atom molecular dynamics simulations of Gal4–DNA interactions. We found a strong enthalpy–entropy compensation, by which the binding of Gal4 to its cognate sequence entails a DNA bending and a striking conformational freezing, which could be instrumental in the biological function of Gal4.
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Affiliation(s)
- Thomas Carzaniga
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università di Milano, 20054 Segrate (MI), Italy; (T.C.); (L.C.); (L.V.); (G.N.)
| | - Giuliano Zanchetta
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università di Milano, 20054 Segrate (MI), Italy; (T.C.); (L.C.); (L.V.); (G.N.)
- Correspondence: (G.Z.); (M.B.); (T.B.)
| | - Elisa Frezza
- CiTCoM, CNRS, Université de Paris, F-75006 Paris, France;
| | - Luca Casiraghi
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università di Milano, 20054 Segrate (MI), Italy; (T.C.); (L.C.); (L.V.); (G.N.)
| | - Luka Vanjur
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università di Milano, 20054 Segrate (MI), Italy; (T.C.); (L.C.); (L.V.); (G.N.)
| | - Giovanni Nava
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università di Milano, 20054 Segrate (MI), Italy; (T.C.); (L.C.); (L.V.); (G.N.)
| | | | - Giorgio Dieci
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università di Parma, 43124 Parma, Italy;
| | - Marco Buscaglia
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università di Milano, 20054 Segrate (MI), Italy; (T.C.); (L.C.); (L.V.); (G.N.)
- Correspondence: (G.Z.); (M.B.); (T.B.)
| | - Tommaso Bellini
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università di Milano, 20054 Segrate (MI), Italy; (T.C.); (L.C.); (L.V.); (G.N.)
- Correspondence: (G.Z.); (M.B.); (T.B.)
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11
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Klakamp SL, Drake AW. Miscalculating Equilibrium Constants for Multivalent Protein Complexes: Site-Binding Concentration or Protein Molecular Concentration? J Pharm Sci 2021; 110:2585-2589. [PMID: 33831440 DOI: 10.1016/j.xphs.2021.03.026] [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: 02/05/2021] [Revised: 03/26/2021] [Accepted: 03/30/2021] [Indexed: 11/16/2022]
Abstract
Because the authors continue to note instances in the scientific literature of failure to use the correct receptor binding site concentration for determining binding constants, herein we discuss the fundamental concepts that need to be considered to determine correct binding constants or conversely calculate accurate reactant concentrations with known equilibrium constants. We also show the derivation and analytical solutions of the cubic and quartic equations that give the exact free ligand concentration in bivalent and trivalent receptor systems at equilibrium as a function of the macroscopic equilibrium dissociation constants and the total concentrations of ligand and multivalent protein. These equations and solutions strongly reemphasize the critical dependency of deriving the correct concentrations of bound or free ligand and multivalent protein on the choice of the correct concentration basis for the multivalent protein, which is in turn dependent upon the type of equilibrium constant used. These results demonstrate the importance of choosing the proper multivalent protein concentration for the determination of either valid microscopic or valid macroscopic equilibrium dissociation constants from binding isotherms of ligand-multivalent protein complexes.
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Affiliation(s)
- Scott L Klakamp
- Coherus BioSciences, 1000 Avenida Acaso, Camarillo, CA 93012, United States.
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12
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Mamer SB, Page P, Murphy M, Wang J, Gallerne P, Ansari A, Imoukhuede PI. The Convergence of Cell-Based Surface Plasmon Resonance and Biomaterials: The Future of Quantifying Bio-molecular Interactions-A Review. Ann Biomed Eng 2020; 48:2078-2089. [PMID: 31811474 PMCID: PMC8637426 DOI: 10.1007/s10439-019-02429-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 11/29/2019] [Indexed: 12/20/2022]
Abstract
Cell biology is driven by complex networks of biomolecular interactions. Characterizing the kinetic and thermodynamic properties of these interactions is crucial to understanding their role in different physiological processes. Surface plasmon resonance (SPR)-based approaches have become a key tool in quantifying biomolecular interactions, however conventional approaches require isolating the interacting components from the cellular system. Cell-based SPR approaches have recently emerged, promising to enable precise measurements of biomolecular interactions within their normal biological context. Two major approaches have been developed, offering their own advantages and limitations. These approaches currently lack a systematic exploration of 'best practices' like those existing for traditional SPR experiments. Toward this end, we describe the two major approaches, and identify the experimental parameters that require exploration, and discuss the experimental considerations constraining the optimization of each. In particular, we discuss the requirements of future biomaterial development needed to advance the cell-based SPR technique.
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Affiliation(s)
- Spencer B Mamer
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | | | | | - Jiaojiao Wang
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Pierrick Gallerne
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Ecole Centrale de Lille, Villeneuve d'Ascq, Hauts-De-France, France
| | - Ali Ansari
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - P I Imoukhuede
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, USA.
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13
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Daub H, Traxler L, Ismajli F, Groitl B, Itzen A, Rant U. The trimer to monomer transition of Tumor Necrosis Factor-Alpha is a dynamic process that is significantly altered by therapeutic antibodies. Sci Rep 2020; 10:9265. [PMID: 32518229 PMCID: PMC7283243 DOI: 10.1038/s41598-020-66123-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 05/12/2020] [Indexed: 11/09/2022] Open
Abstract
The cytokine tumor necrosis factor-alpha (TNF-α) readily forms homotrimers at sub-nM concentrations to promote inflammation. For the treatment of inflammatory diseases with upregulated levels of TNF-α, a number of therapeutic antibodies are currently used as scavengers to reduce the active TNF-α concentration in patients. Despite their clinical success, the mode-of-action of different antibody formats with regard to a stabilization of the trimeric state is not entirely understood. Here, we use a biosensor with dynamic nanolevers to analyze the monomeric and trimeric states of TNF-α together with the binding kinetics of therapeutic biologics. The intrinsic trimer-to-monomer decay rate k = 1.7 × 10−3 s−1 could be measured directly using a microfluidic system, and antibody binding affinities were analyzed in the pM range. Trimer stabilization effects are quantified for Adalimumab, Infliximab, Etanercept, Certolizumab, Golimumab for bivalent and monovalent binding formats. Clear differences in trimer stabilization are observed, which may provide a deeper insight into the mode-of-action of TNF-α scavengers.
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Affiliation(s)
- Herwin Daub
- Dynamic Biosensors GmbH, Lochhamer Strasse 15, 82152, Martinsried, Germany. .,Center for Integrated Protein Science Munich, Technische Universität München, Department Chemistry, Lichtenbergstrasse 4, 85748, Garching, Germany.
| | - Lukas Traxler
- Dynamic Biosensors GmbH, Lochhamer Strasse 15, 82152, Martinsried, Germany
| | - Fjolla Ismajli
- Dynamic Biosensors GmbH, Lochhamer Strasse 15, 82152, Martinsried, Germany
| | - Bastian Groitl
- Dynamic Biosensors GmbH, Lochhamer Strasse 15, 82152, Martinsried, Germany
| | - Aymelt Itzen
- Center for Integrated Protein Science Munich, Technische Universität München, Department Chemistry, Lichtenbergstrasse 4, 85748, Garching, Germany.,Department of Biochemistry and Signaltransduction, University Medical Centre Hamburg-Eppendorf (UKE), Martinistrasse 52, 20246, Hamburg, Germany
| | - Ulrich Rant
- Dynamic Biosensors GmbH, Lochhamer Strasse 15, 82152, Martinsried, Germany
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14
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Mesoporous Pd@Pt nanoparticle-linked immunosorbent assay for detection of atrazine. Anal Chim Acta 2020; 1116:36-44. [DOI: 10.1016/j.aca.2020.03.045] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 03/16/2020] [Accepted: 03/22/2020] [Indexed: 11/19/2022]
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15
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PCR incorporation of dUMPs modified with aromatic hydrocarbon substituents of different hydrophilicities: Synthesis of C5-modified dUTPs and PCR studies using Taq, Tth, Vent (exo-) and Deep Vent (exo-) polymerases. Bioorg Chem 2020; 99:103829. [PMID: 32299018 DOI: 10.1016/j.bioorg.2020.103829] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 03/25/2020] [Accepted: 04/05/2020] [Indexed: 02/07/2023]
Abstract
Deoxyuridine triphosphate derivatives (dUTPs) modified at the C5 position of the pyrimidine ring with various aromatic hydrocarbon substituents of different hydrophilicities have been synthesized. The aromatic hydrocarbon substituents were attached to dUTPs via a CHCHCH2NHCOCH2 linker. The efficiency of the PCR incorporation of modified dUMPs using Taq, Tth, Vent (exo-) and Deep Vent (exo-) polymerases and a model DNA template containing one, two and three adjacent adenine nucleotides at three different sites within the sequence was investigated. For all the polymerases used, the yield of the modified PCR product was significantly increased with increasing hydrophilicity of the aromatic hydrocarbon substituent. In particular, for the above polymerases, the efficiency of the incorporation of dUMPs modified with the most hydrophilic of the studied aromatic hydrocarbon substituents, a 4-hydroxyphenyl residue, was 60-85% of the efficiency of dTMP incorporation. At the same time, the relative efficiencies of the incorporation of dUMPs modified with 2-, 4-methoxyphenyl, phenyl and 4-nitrophenyl substituents ranged from 20 to 50% and were 2-18% for the 1-naphthalene and 4-biphenyl groups, which were the most hydrophobic of the studied aromatic hydrocarbon substituents.
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16
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Brown ME, Bedinger D, Lilov A, Rathanaswami P, Vásquez M, Durand S, Wallace-Moyer I, Zhong L, Nett JH, Burnina I, Caffry I, Lynaugh H, Sinclair M, Sun T, Bukowski J, Xu Y, Abdiche YN. Assessing the binding properties of the anti-PD-1 antibody landscape using label-free biosensors. PLoS One 2020; 15:e0229206. [PMID: 32134960 PMCID: PMC7058304 DOI: 10.1371/journal.pone.0229206] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 01/31/2020] [Indexed: 12/21/2022] Open
Abstract
Here we describe an industry-wide collaboration aimed at assessing the binding properties of a comprehensive panel of monoclonal antibodies (mAbs) against programmed cell death protein 1 (PD-1), an important checkpoint protein in cancer immunotherapy and validated therapeutic target, with well over thirty unique mAbs either in clinical development or market-approved in the United States, the European Union or China. The binding kinetics of the PD-1/mAb interactions were measured by surface plasmon resonance (SPR) using a Carterra LSA instrument and the results were compared to data collected on a Biacore 8K. The effect of chip type on the SPR-derived binding rate constants and affinities were explored and the results compared with solution affinities from Meso Scale Discovery (MSD) and Kinetic Exclusion Assay (KinExA) experiments. When using flat chip types, the LSA and 8K platforms yielded near-identical kinetic rate and affinity constants that matched solution phase values more closely than those produced on 3D-hydrogels. Of the anti-PD-1 mAbs tested, which included a portion of those known to be in clinical development or approved, the affinities spanned from single digit picomolar to nearly 425 nM, challenging the dynamic range of our methods. The LSA instrument was also used to perform epitope binning and ligand competition studies which revealed over ten unique competitive binding profiles within this group of mAbs.
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Affiliation(s)
- Michael E. Brown
- Department of Protein Analytics, Adimab, Lebanon, NH, United States of America
- * E-mail: (MEB); (YNA)
| | | | - Asparouh Lilov
- Department of Protein Analytics, Adimab, Lebanon, NH, United States of America
| | | | - Maximiliano Vásquez
- Department of Computational Biology, Adimab, Palo Alto, CA, United States of America
| | - Stéphanie Durand
- Department of High Throughput Expression, Adimab, Lebanon, NH, United States of America
| | - Ian Wallace-Moyer
- Department of High Throughput Expression, Adimab, Lebanon, NH, United States of America
| | - Lihui Zhong
- Department of High Throughput Expression, Adimab, Lebanon, NH, United States of America
| | - Juergen H. Nett
- Department of High Throughput Expression, Adimab, Lebanon, NH, United States of America
| | - Irina Burnina
- Department of Protein Analytics, Adimab, Lebanon, NH, United States of America
| | - Isabelle Caffry
- Department of Protein Analytics, Adimab, Lebanon, NH, United States of America
| | - Heather Lynaugh
- Department of Protein Analytics, Adimab, Lebanon, NH, United States of America
| | - Melanie Sinclair
- Department of Protein Analytics, Adimab, Lebanon, NH, United States of America
| | - Tingwan Sun
- Department of Protein Analytics, Adimab, Lebanon, NH, United States of America
| | - John Bukowski
- Department of Antibody Discovery, Adimab, Lebanon, NH, United States of America
| | - Yingda Xu
- Department of Protein Analytics, Adimab, Lebanon, NH, United States of America
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17
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Kamat V, Rafique A, Huang T, Olsen O, Olson W. The impact of different human IgG capture molecules on the kinetics analysis of antibody-antigen interaction. Anal Biochem 2020; 593:113580. [PMID: 31926892 DOI: 10.1016/j.ab.2020.113580] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Accepted: 01/06/2020] [Indexed: 12/12/2022]
Abstract
Surface plasmon resonance (SPR) is a well-established method to characterize biomolecular interactions and is widely used in drug discovery and development. Here, we demonstrate that capture surfaces profoundly impact the binding kinetics parameters that are measured for antibody-antigen interactions. Six unique antibody-antigen interactions were characterized using eight different anti-human IgG capture surfaces. The antigen binding affinities for six different human monoclonal antibodies (hmAbs) captured using three different goat anti-human Fc (AHC) polyclonal antibody (pAb) surfaces were in reasonable agreement (3-7-fold weaker) with those measured by kinetic exclusion assay (KinExA). In contrast, up to 81, 32, 489, 2826, and 219-fold weaker antigen binding affinities were measured using mouse AHC mAb, Protein G, Protein A, Protein A/G, and Protein L surfaces, respectively. Protein A, Protein A/G and Protein G interacted with the Fab of hmAbs, possibly affecting antigen binding to hmAbs captured over these surfaces. Additional studies revealed that mouse AHC mAb binds hmAbs with a weak affinity (5.5-36.3 nM) and t½ values of 1.4-3.3min, compared to the sub-nanomolar affinities of the goat AHC pAbs. These results emphasize the value of measuring binding kinetics of the capture molecule before immobilizing them onto the sensor surface to perform capture kinetics assays on label-free biosensors.
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Affiliation(s)
- Vishal Kamat
- Biomolecular HTS Center, Therapeutic Proteins, Regeneron Pharmaceuticals, Tarrytown, NY, USA.
| | - Ashique Rafique
- Biomolecular HTS Center, Therapeutic Proteins, Regeneron Pharmaceuticals, Tarrytown, NY, USA
| | - Tammy Huang
- Therapeutic Proteins, Regeneron Pharmaceuticals, Tarrytown, NY, USA
| | - Olav Olsen
- Therapeutic Proteins, Regeneron Pharmaceuticals, Tarrytown, NY, USA
| | - William Olson
- Therapeutic Proteins, Regeneron Pharmaceuticals, Tarrytown, NY, USA
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18
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Zwaagstra JC, Sulea T, Baardsnes J, Radinovic S, Cepero-Donates Y, Robert A, O’Connor-McCourt MD, Tikhomirov IA, Jaramillo ML. Binding and functional profiling of antibody mutants guides selection of optimal candidates as antibody drug conjugates. PLoS One 2019; 14:e0226593. [PMID: 31891584 PMCID: PMC6938348 DOI: 10.1371/journal.pone.0226593] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 11/30/2019] [Indexed: 12/15/2022] Open
Abstract
An increasingly appreciated conundrum in the discovery of antibody drug conjugates (ADCs) is that an antibody that was selected primarily for strong binding to its cancer target may not serve as an optimal ADC. In this study, we performed mechanistic cell-based experiments to determine the correlation between antibody affinity, avidity, internalization and ADC efficacy. We used structure-guided design to assemble a panel of antibody mutants with predicted Her2 affinities ranging from higher to lower relative to the parent antibody, Herceptin. These antibodies were ranked for binding via SPR and via flow-cytometry on high-Her2 SKOV3 cells and low-Her2 MCF7 cells, the latter acting as a surrogate for low-Her2 normal cells. A subpanel of variants, representative of different Her2-binding affinities (2 strong, 2 moderate and 3 weak), were further screened via high-content imaging for internalization efficacies in high versus low-Her2 cells. Finally, these antibodies were evaluated in ADC cytotoxicity screening assays (using DM1 and MMAE secondary antibodies) and as antibody-drug conjugates (DM1 and PNU159682). Our results identified specific but weak Her2-binding variants as optimal candidates for developing DM1 and PNU ADCs since they exhibited high potencies (low to sub-nM) in high-Her2 SKOV3 cells and low toxicities in low-Her2 cells. The 2 strong-affinity variants were highly potent in SKOV3 cells but also showed significant toxicities in low-Her2 cells and therefore are predicted to be toxic in normal tissues. Our findings show that pharmacological profiling of an antibody library in multiple binding and functional assays allows for selection of optimal ADCs.
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Affiliation(s)
- John C. Zwaagstra
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
- * E-mail: (JZ); (MJ)
| | - Traian Sulea
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Jason Baardsnes
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Stevo Radinovic
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Yuneivy Cepero-Donates
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Alma Robert
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | | | | | - Maria Luz. Jaramillo
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
- * E-mail: (JZ); (MJ)
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19
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Sinn S, Spuling E, Bräse S, Biedermann F. Rational design and implementation of a cucurbit[8]uril-based indicator-displacement assay for application in blood serum. Chem Sci 2019; 10:6584-6593. [PMID: 31367309 PMCID: PMC6628674 DOI: 10.1039/c9sc00705a] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Accepted: 05/31/2019] [Indexed: 12/14/2022] Open
Abstract
In this study, we report the first supramolecular indicator displacement assay (IDA) based on cucurbit[n]uril (CBn) host and a [2.2]paracyclophane derivative as indicator that is operational in blood serum.
In this study, we report the first supramolecular indicator-displacement assay (IDA) based on cucurbit[n]uril (CBn) hosts that is operational in blood serum. Rational design principles for host–guest chemosensing in competitively binding media were derived through detailed mathematical simulations. It was shown that currently known CBn-based chemosensing ensembles are not suited for use in highly competitive matrices such as blood serum. Conversely, the simulations indicated that a combination of cucurbit[8]uril (CB8) and an ultra-high affinity dye would be a promising IDA reporter pair for the detection of Alzheimer's drug memantine in blood serum. Therefore, a novel class of [2.2]paracyclophane-derived indicator dyes for the host CB8 was developed that possesses one of the highest host–guest affinities (Ka > 1012 M–1 in water) known in supramolecular host–guest chemistry, and which provides a large Stokes shift (up to 200 nm). The novel IDA was then tested for the detection of memantine in blood serum in a physiologically relevant sub- to low micromolar concentration range.
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Affiliation(s)
- Stephan Sinn
- Karlsruhe Institute of Technology (KIT) , Institute of Nanotechnology (INT) , Hermann-von-Helmholtz-Platz 1 , 76344 Eggenstein-Leopoldshafen , Germany .
| | - Eduard Spuling
- Karlsruhe Institute of Technology (KIT) , Institute of Organic Chemistry , Fritz-Haber-Weg 6 , 76131 Karlsruhe , Germany
| | - Stefan Bräse
- Karlsruhe Institute of Technology (KIT) , Institute of Organic Chemistry , Fritz-Haber-Weg 6 , 76131 Karlsruhe , Germany.,Karlsruhe Institute of Technology (KIT) , Institute of Toxicology and Genetics (ITG) , Hermann-von-Helmholtz-Platz 1 , 76344 Eggenstein-Leopoldshafen , Germany
| | - Frank Biedermann
- Karlsruhe Institute of Technology (KIT) , Institute of Nanotechnology (INT) , Hermann-von-Helmholtz-Platz 1 , 76344 Eggenstein-Leopoldshafen , Germany .
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20
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HiBiT-qIP, HiBiT-based quantitative immunoprecipitation, facilitates the determination of antibody affinity under immunoprecipitation conditions. Sci Rep 2019; 9:6895. [PMID: 31053795 PMCID: PMC6499798 DOI: 10.1038/s41598-019-43319-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 01/31/2019] [Indexed: 12/23/2022] Open
Abstract
The affinity of an antibody for its antigen serves as a critical parameter for antibody evaluation. The evaluation of antibody-antigen affinity is essential for a successful antibody-based assay, particularly immunoprecipitation (IP), due to its strict dependency on antibody performance. However, the determination of antibody affinity or its quantitative determinant, the dissociation constant (Kd), under IP conditions is difficult. In the current study, we used a NanoLuc-based HiBiT system to establish a HiBiT-based quantitative immunoprecipitation (HiBiT-qIP) assay for determining the Kd of antigen-antibody interactions in solution. The HiBiT-qIP method measures the amount of immunoprecipitated proteins tagged with HiBiT in a simple yet quantitative manner. We used this method to measure the Kd values of epitope tag-antibody interactions. To accomplish this, FLAG, HA, V5, PA and Ty1 epitope tags in their monomeric, dimeric or trimeric form were fused with glutathione S-transferase (GST) and the HiBiT peptide, and these tagged GST proteins were mixed with cognate monoclonal antibodies in IP buffer for the assessment of the apparent Kd values. This HiBiT-qIP assay showed a considerable variation in the Kd values among the examined antibody clones. Additionally, the use of epitope tags in multimeric form revealed a copy number-dependent increase in the apparent affinity.
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21
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Yi J, Qin Q, Wang Y, Zhang R, Bi H, Yu S, Liu B, Qiao L. Identification of pathogenic bacteria in human blood using IgG-modified Fe 3O 4 magnetic beads as a sorbent and MALDI-TOF MS for profiling. Mikrochim Acta 2018; 185:542. [PMID: 30415312 DOI: 10.1007/s00604-018-3074-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 10/26/2018] [Indexed: 12/15/2022]
Abstract
A method is described for fast identification of bacteria by combining (a) the enrichment of bacterial cells by using magnetite (Fe3O4) magnetic beads modified with human IgG (IgG@Fe3O4) and (b) MALDI-TOF MS analysis. IgG has affinity to protein A, protein G, protein L and glycans on the surface of bacterial cells, and IgG@Fe3O4. It therefore is applicable to the preconcentration of a range of bacterial species. The feasibility of the method has been demonstrated by collecting six species of pathogenic bacteria (Gram-positives: Staphylococcus aureus and Kocuria rosea; Gram-negatives: Klebsiella pneumoniae, Klebsiella oxytoca, Enterobacter cloacae and Pseudomonas aeruginosa). Bacteria with concentrations as low as 10 CFU·mL-1 in spiked water samples were extracted by this sorbent with recovery rates of >50%. After enrichment, bacteria on the IgG@Fe3O4 sorbent were further identified by MALDI-TOF MS. Bacteria in concentrations as low as 105 CFU in 100 μL of human whole blood can be identified by the method. Compared to other blood culture based tests, the culture time is shortened by 40% (from ~10 h to ~6 h), and the plate culture procedure (overnight) is avoided. After short blood culture, the enrichment and identification can be finished in one hour. The IgG@Fe3O4 is of practical value in clinical diagnosis and may be combined with other identification methods, e.g. PCR, Raman spectroscopy, infrared spectroscopy, etc. Graphical abstract A non-targeted, fast and sensitive assay for bacterial identification from human blood has been developed based on the enrichment of bacteria by IgG@Fe3O4 and identification by MALDI-TOF MS.
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Affiliation(s)
- Jia Yi
- Department of Chemistry, Shanghai Stomatological Hospital, Fudan University, Shanghai, 200000, China
| | - Qin Qin
- Changhai Hospital, The Naval Military Medical University, Shanghai, 200433, China
| | - Yan Wang
- Department of Chemistry, Shanghai Stomatological Hospital, Fudan University, Shanghai, 200000, China
| | - Rutan Zhang
- Department of Chemistry, Shanghai Stomatological Hospital, Fudan University, Shanghai, 200000, China
| | - Hongyan Bi
- College of Food Science and Engineering, Shanghai Ocean University, Shanghai, 201306, China
| | - Shaoning Yu
- Department of Chemistry, Shanghai Stomatological Hospital, Fudan University, Shanghai, 200000, China
| | - Baohong Liu
- Department of Chemistry, Shanghai Stomatological Hospital, Fudan University, Shanghai, 200000, China
| | - Liang Qiao
- Department of Chemistry, Shanghai Stomatological Hospital, Fudan University, Shanghai, 200000, China.
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22
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AlRabiah H, Hamidaddin MA, Darwish IA. Automated flow fluorescent noncompetitive immunoassay for measurement of human plasma levels of monoclonal antibodies used for immunotherapy of cancers with KinExA™ 3200 biosensor. Talanta 2018; 192:331-338. [PMID: 30348399 DOI: 10.1016/j.talanta.2018.09.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 09/05/2018] [Accepted: 09/05/2018] [Indexed: 12/18/2022]
Abstract
This study describes, for the first time, the development of an automated sensitive flow fluorescent noncompetitive immunoassay based on kinetic-exclusion analysis (KinExA) for the quantitative determination of human plasma levels of monoclonal antibodies (mAbs) used for cancer immunotherapy. The assay was adapted on KinExA™ 3200 biosensor and optimized and validated for bevacizumab (BEV) and cetuximab (CET), as representative examples of the mAbs, using their specific antigens. These antigens were the human vascular endothelial growth factor (VEGF) and epidermal growth factor receptor (EGFR) for BEV and CET, respectively. The limits of detection were 1.28 and 52.64 ng mL-1 for BEV and CET, respectively. The accuracy of the assay was demonstrated with analytical recovery of analytes from spiked plasma at 96.2-104.3 and 96.8-105.3% for BEV and CET, respectively. The precision of the assay was satisfactory as shown by relative standard deviation (RSD) at 2.2-5.7 and 2.5-6.1% for assay of BEV and CET, respectively. The high sensitivity of the assay allowed the use of very small volumes (~ 1 µL) of plasma sample for analysis. Automated analysis by the proposed KinExA-based assay facilitates the processing of large numbers of mAbs-containing specimens in studies of pharmacokinetics (PK), pharmacodynamics (PD), and therapeutic drug monitoring (TDM) of therapeutic mAbs. The proposed assay can be used to overcome the problems encountered in the existing conventional immunoassays for mAbs.
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Affiliation(s)
- Haitham AlRabiah
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
| | - Mohammed A Hamidaddin
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia; Department of Medicinal and Analytical Chemistry, Faculty of Pharmacy, Sana'a University, Sana'a, Yemen
| | - Ibrahim A Darwish
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia.
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23
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Quinn JG, Pitts KE, Steffek M, Mulvihill MM. Determination of Affinity and Residence Time of Potent Drug-Target Complexes by Label-free Biosensing. J Med Chem 2018; 61:5154-5161. [PMID: 29772180 DOI: 10.1021/acs.jmedchem.7b01829] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Prolonged drug-target occupancy has become increasingly important in lead optimization, and biophysical assays that measure residence time are in high demand. Here we report a practical label-free assay methodology that provides kinetic and affinity measurements suitable for most target classes without long preincubations and over comparatively short sample contact times. The method, referred to as a "chaser" assay, has been applied to three sets of unrelated kinase/inhibitor panels in order to measure the residence times, where correlation with observed efficacy was suspected. A lower throughput chaser assay measured a residence time of 3.6 days ±3.4% (95% CI) and provided single digit pM sensitivity. A higher throughput chaser methodology enabled a maximum capacity of 108 compounds in duplicate/day with an upper residence time limit of 9 h given an assay dissociation time of 34 min.
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Affiliation(s)
- John G Quinn
- Biophysical group, Biochemical and Cellular Pharmacology , Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | - Keith E Pitts
- Biophysical group, Biochemical and Cellular Pharmacology , Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | - Micah Steffek
- Biophysical group, Biochemical and Cellular Pharmacology , Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | - Melinda M Mulvihill
- Biophysical group, Biochemical and Cellular Pharmacology , Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
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24
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Multiple epitope presentation and surface density control enabled by chemoselective immobilization lead to enhanced performance in IgE-binding fingerprinting on peptide microarrays. Anal Chim Acta 2017; 983:189-197. [DOI: 10.1016/j.aca.2017.06.027] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 06/09/2017] [Accepted: 06/16/2017] [Indexed: 11/17/2022]
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25
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Ljubimova JY, Sun T, Mashouf L, Ljubimov AV, Israel LL, Ljubimov VA, Falahatian V, Holler E. Covalent nano delivery systems for selective imaging and treatment of brain tumors. Adv Drug Deliv Rev 2017; 113:177-200. [PMID: 28606739 PMCID: PMC5578712 DOI: 10.1016/j.addr.2017.06.002] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 06/07/2017] [Indexed: 02/06/2023]
Abstract
Nanomedicine is a rapidly evolving form of therapy that holds a great promise for superior drug delivery efficiency and therapeutic efficacy than conventional cancer treatment. In this review, we attempt to cover the benefits and the limitations of current nanomedicines with special attention to covalent nano conjugates for imaging and drug delivery in the brain. The improvement in brain tumor treatment remains dismal despite decades of efforts in drug development and patient care. One of the major obstacles in brain cancer treatment is the poor drug delivery efficiency owing to the unique blood-brain barrier (BBB) in the CNS. Although various anti-cancer agents are available to treat tumors outside of the CNS, the majority fails to cross the BBB. In this regard, nanomedicines have increasingly drawn attention due to their multi-functionality and versatility. Nano drugs can penetrate BBB and other biological barriers, and selectively accumulate in tumor cells, while concurrently decreasing systemic toxicity.
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Affiliation(s)
- Julia Y Ljubimova
- Nanomedicine Research Center, Department of Neurosurgery, Cedars-Sinai Medical Center, 8700 Beverly Blvd., AHSP, Los Angeles, CA 90048, USA.
| | - Tao Sun
- Nanomedicine Research Center, Department of Neurosurgery, Cedars-Sinai Medical Center, 8700 Beverly Blvd., AHSP, Los Angeles, CA 90048, USA
| | - Leila Mashouf
- Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA
| | - Alexander V Ljubimov
- Department of Biomedical Sciences, Board of Governors Regenerative Medicine Institute, Los Angeles, CA 90048, USA
| | - Liron L Israel
- Nanomedicine Research Center, Department of Neurosurgery, Cedars-Sinai Medical Center, 8700 Beverly Blvd., AHSP, Los Angeles, CA 90048, USA
| | - Vladimir A Ljubimov
- Department of Neurosurgery and Brain Repair, University of South Florida, 2 Tampa General Circle, Tampa, FL 33606, USA
| | - Vida Falahatian
- Duke University School of Medicine, Department of Biostatistics and Bioinformatics, Clinical Research Training Program (CRTP), 2424 Erwin Road, Suite 1102, Hock Plaza Box 2721, Durham, NC 27710, USA
| | - Eggehard Holler
- Nanomedicine Research Center, Department of Neurosurgery, Cedars-Sinai Medical Center, 8700 Beverly Blvd., AHSP, Los Angeles, CA 90048, USA; Institut für Biophysik und Physikalische Biochemie, Universität Regensburg, D-93040 Regensburg, Germany
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26
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Abstract
Monoclonal antibodies (MAbs) have become a substantial part of many pharmaceutical company portfolios. However, the development process of MAbs for clinical use is quite different than for small-molecule drugs. MAb development programs require careful interdisciplinary evaluations to ensure the pharmacology of both the MAb and the target antigen are well-understood. Selection of appropriate preclinical species must be carefully considered and the potential development of anti-drug antibodies (ADA) during these early studies can limit the value and complicate the performance and possible duration of preclinical studies. In human studies, many of the typical pharmacology studies such as renal or hepatic impairment evaluations may not be needed but the pharmacokinetics and pharmacodynamics of these agents is complex, often necessitating more comprehensive evaluation of clinical data and more complex bioanalytical assays than might be used for small molecules. This paper outlines concerns and strategies for development of MAbs from the early in vitro assessments needed through preclinical and clinical development. This review focuses on how to develop, submit, and comply with regulatory requirements for MAb therapeutics.
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Abstract
The use of optical biosensors for studying macromolecular interactions is gaining increasing popularity. In one study, 1514 papers that involved the application of biosensor data were identified for the year 2009 alone (Rich and Myszka, J Mol Recognit 24:892-914, 2011), the sheer volume and variety of which present a daunting task for the burgeoning biosensor user to accumulate and decipher. This chapter is designed to provide the reader with the tools necessary to prepare, design, and efficiently execute a kinetic experiment on Biacore. It is written to guide the Biacore user through basic theory, system maintenance, and assay setup while also offering some practical tips that we find useful for Biacore-based studies. Many kinetic-based screening assays require rigorous sample preparation and purification prior to analysis. To highlight these procedures, this protocol describes the kinetic characterization of single chain Fv (scFv) antibody fragments from crude bacterial lysates using an antibody affinity capture approach. Even though we specifically describe the capture of HA-tagged scFv antibody fragments to an anti-HA tag monoclonal antibody-immobilized surface prior to kinetic analysis, the same methodologies are universally applicable and can be used for practically any affinity pair and most Biacore systems.
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Affiliation(s)
- Paul Leonard
- Biomedical Diagnostics Institute, Dublin City University, Dublin 9, Ireland
- School of Biotechnology, Dublin City University, Dublin 9, Ireland
- National Centre for Sensor Research, Dublin City University, Dublin 9, Ireland
| | - Stephen Hearty
- Biomedical Diagnostics Institute, Dublin City University, Dublin 9, Ireland
- School of Biotechnology, Dublin City University, Dublin 9, Ireland
- National Centre for Sensor Research, Dublin City University, Dublin 9, Ireland
| | - Hui Ma
- Biomedical Diagnostics Institute, Dublin City University, Dublin 9, Ireland
| | - Richard O'Kennedy
- Biomedical Diagnostics Institute, Dublin City University, Dublin 9, Ireland.
- School of Biotechnology, Dublin City University, Dublin 9, Ireland.
- National Centre for Sensor Research, Dublin City University, Dublin 9, Ireland.
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Wang X, McKay P, Yee LT, Dutina G, Hass PE, Nijem I, Allison D, Cowan KJ, Lin K, Quarmby V, Yang J. Impact of SPR biosensor assay configuration on antibody: Neonatal Fc receptor binding data. MAbs 2016; 9:319-332. [PMID: 28001487 DOI: 10.1080/19420862.2016.1261774] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Binding interactions with the neonatal Fc receptor (FcRn) are one determinant of pharmacokinetic properties of recombinant human monoclonal antibody (rhumAb) therapeutics, and a conserved binding motif in the crystallizable fragment (Fc) region of IgG molecules interacts with FcRn. Surface plasmon resonance (SPR) biosensor assays are often used to characterize interactions between FcRn and rhumAb therapeutics. In such assays, generally either the rhumAb (format 1) or the FcRn protein (format 2) is immobilized on a biosensor chip. However, because evidence suggests that, in some cases, the variable domains of a rhumAb may also affect FcRn binding, we evaluated the effect of SPR assay configuration on binding data. We sought to assess FcRn binding properties of 2 rhumAbs (rhumAb1 and rhumAb2) to FcRn proteins using these 2 biosensor assay formats. The two rhumAbs have greater than 99% sequence identity in the Fc domain but differ in their Fab regions. rhumAb2 contains a positively charged patch in the variable domain that is absent in rhumAb1. Our results showed that binding of rhumAb1 to FcRn was independent of biosensor assay configuration, while binding of rhumAb2 to FcRn was highly SPR assay configuration dependent. Further investigations revealed that the format dependency of rhumAb2-FcRn binding is linked to the basic residues that form a positively charged patch in the variable domain of rhumAb2. Our work highlights the importance of analyzing rhumAb-FcRn binding interactions using 2 alternate SPR biosensor assay configurations. This approach may also provide a simple way to identify the potential for non-Fc-driven FcRn binding interactions in otherwise typical IgGs.
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Affiliation(s)
- Xiangdan Wang
- a BioAnalytical Sciences, Genentech , South San Francisco , CA , USA
| | - Patrick McKay
- b Technical Development, Genentech , South San Francisco , CA , USA
| | - Liliana T Yee
- b Technical Development, Genentech , South San Francisco , CA , USA
| | - George Dutina
- c Department of Early Stage Cell Culture , Genentech , South San Francisco , CA , USA
| | - Philip E Hass
- d Protein Chemistry, Genentech , South San Francisco , CA , USA
| | - Ihsan Nijem
- a BioAnalytical Sciences, Genentech , South San Francisco , CA , USA
| | - David Allison
- e Clinical Pharmacology, Genentech , South San Francisco , CA , USA
| | - Kyra J Cowan
- a BioAnalytical Sciences, Genentech , South San Francisco , CA , USA
| | - Kevin Lin
- f Analytical Operations, Genentech , South San Francisco , CA , USA
| | - Valerie Quarmby
- a BioAnalytical Sciences, Genentech , South San Francisco , CA , USA
| | - Jihong Yang
- a BioAnalytical Sciences, Genentech , South San Francisco , CA , USA
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29
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Bastos VA, Gomes-Neto F, Perales J, Neves-Ferreira AGC, Valente RH. Natural Inhibitors of Snake Venom Metalloendopeptidases: History and Current Challenges. Toxins (Basel) 2016; 8:toxins8090250. [PMID: 27571103 PMCID: PMC5037476 DOI: 10.3390/toxins8090250] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2016] [Revised: 08/11/2016] [Accepted: 08/15/2016] [Indexed: 01/13/2023] Open
Abstract
The research on natural snake venom metalloendopeptidase inhibitors (SVMPIs) began in the 18th century with the pioneering work of Fontana on the resistance that vipers exhibited to their own venom. During the past 40 years, SVMPIs have been isolated mainly from the sera of resistant animals, and characterized to different extents. They are acidic oligomeric glycoproteins that remain biologically active over a wide range of pH and temperature values. Based on primary structure determination, mammalian plasmatic SVMPIs are classified as members of the immunoglobulin (Ig) supergene protein family, while the one isolated from muscle belongs to the ficolin/opsonin P35 family. On the other hand, SVMPIs from snake plasma have been placed in the cystatin superfamily. These natural antitoxins constitute the first line of defense against snake venoms, inhibiting the catalytic activities of snake venom metalloendopeptidases through the establishment of high-affinity, non-covalent interactions. This review presents a historical account of the field of natural resistance, summarizing its main discoveries and current challenges, which are mostly related to the limitations that preclude three-dimensional structural determinations of these inhibitors using “gold-standard” methods; perspectives on how to circumvent such limitations are presented. Potential applications of these SVMPIs in medicine are also highlighted.
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Affiliation(s)
- Viviane A Bastos
- Laboratory of Toxinology, Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro 21040-900, Brazil.
- National Institute of Science and Technology on Toxins (INCTTOX), CNPq, Brasilia 71605-001, Brazil.
| | - Francisco Gomes-Neto
- Laboratory of Toxinology, Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro 21040-900, Brazil.
- National Institute of Science and Technology on Toxins (INCTTOX), CNPq, Brasilia 71605-001, Brazil.
| | - Jonas Perales
- Laboratory of Toxinology, Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro 21040-900, Brazil.
- National Institute of Science and Technology on Toxins (INCTTOX), CNPq, Brasilia 71605-001, Brazil.
| | - Ana Gisele C Neves-Ferreira
- Laboratory of Toxinology, Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro 21040-900, Brazil.
- National Institute of Science and Technology on Toxins (INCTTOX), CNPq, Brasilia 71605-001, Brazil.
| | - Richard H Valente
- Laboratory of Toxinology, Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro 21040-900, Brazil.
- National Institute of Science and Technology on Toxins (INCTTOX), CNPq, Brasilia 71605-001, Brazil.
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30
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Hunter SA, Cochran JR. Cell-Binding Assays for Determining the Affinity of Protein-Protein Interactions: Technologies and Considerations. Methods Enzymol 2016; 580:21-44. [PMID: 27586327 PMCID: PMC6067677 DOI: 10.1016/bs.mie.2016.05.002] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Determining the equilibrium-binding affinity (Kd) of two interacting proteins is essential not only for the biochemical study of protein signaling and function but also for the engineering of improved protein and enzyme variants. One common technique for measuring protein-binding affinities uses flow cytometry to analyze ligand binding to proteins presented on the surface of a cell. However, cell-binding assays require specific considerations to accurately quantify the binding affinity of a protein-protein interaction. Here we will cover the basic assumptions in designing a cell-based binding assay, including the relevant equations and theory behind determining binding affinities. Further, two major considerations in measuring binding affinities-time to equilibrium and ligand depletion-will be discussed. As these conditions have the potential to greatly alter the Kd, methods through which to avoid or minimize them will be provided. We then outline detailed protocols for performing direct- and competitive-binding assays against proteins displayed on the surface of yeast or mammalian cells that can be used to derive accurate Kd values. Finally, a comparison of cell-based binding assays to other types of binding assays will be presented.
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Affiliation(s)
- S A Hunter
- Stanford University, Stanford, CA, United States
| | - J R Cochran
- Stanford University, Stanford, CA, United States.
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31
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Thura M, Al-Aidaroos AQO, Yong WP, Kono K, Gupta A, Lin YB, Mimura K, Thiery JP, Goh BC, Tan P, Soo R, Hong CW, Wang L, Lin SJ, Chen E, Rha SY, Chung HC, Li J, Nandi S, Yuen HF, Zhang SD, Guan YK, So J, Zeng Q. PRL3-zumab, a first-in-class humanized antibody for cancer therapy. JCI Insight 2016; 1:e87607. [PMID: 27699276 DOI: 10.1172/jci.insight.87607] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Novel, tumor-specific drugs are urgently needed for a breakthrough in cancer therapy. Herein, we generated a first-in-class humanized antibody (PRL3-zumab) against PRL-3, an intracellular tumor-associated phosphatase upregulated in multiple human cancers, for unconventional cancer immunotherapies. We focused on gastric cancer (GC), wherein elevated PRL-3 mRNA levels significantly correlated with shortened overall survival of GC patients. PRL-3 protein was overexpressed in 85% of fresh-frozen clinical gastric tumor samples examined but not in patient-matched normal gastric tissues. Using human GC cell lines, we demonstrated that PRL3-zumab specifically blocked PRL-3+, but not PRL-3-, orthotopic gastric tumors. In this setting, PRL3-zumab had better therapeutic efficacy as a monotherapy, rather than simultaneous combination with 5-fluorouracil or 5-fluorouracil alone. PRL3-zumab could also prevent PRL-3+ tumor recurrence. Mechanistically, we found that intracellular PRL-3 antigens could be externalized to become "extracellular oncotargets" that serve as bait for PRL3-zumab binding to potentially bridge and recruit immunocytes into tumor microenvironments for killing effects on cancer cells. In summary, our results document a comprehensive cancer therapeutic approach to specific antibody-targeted therapy against the PRL-3 oncotarget as a case study for developing antibodies against other intracellular targets in drug discovery.
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Affiliation(s)
- Min Thura
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore
| | | | - Wei Peng Yong
- Department of Haematology-Oncology, National University Cancer Institute, Singapore.,Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Koji Kono
- Cancer Science Institute of Singapore, National University of Singapore, Singapore.,Division of General Surgery (Upper Gastrointestinal Surgery), National University Hospital, Singapore
| | - Abhishek Gupta
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore
| | - You Bin Lin
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Kousaku Mimura
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Jean Paul Thiery
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore.,Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Boon Cher Goh
- Department of Haematology-Oncology, National University Cancer Institute, Singapore.,Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Patrick Tan
- Genome Institute of Singapore, A*STAR, Singapore
| | - Ross Soo
- Department of Haematology-Oncology, National University Cancer Institute, Singapore.,Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | | | - Lingzhi Wang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | | | - Elya Chen
- Division of General Surgery (Upper Gastrointestinal Surgery), National University Hospital, Singapore
| | - Sun Young Rha
- Department of Internal Medicine, Yonsei Cancer Research Institute, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, South Korea
| | - Hyun Cheol Chung
- Department of Internal Medicine, Yonsei Cancer Research Institute, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, South Korea
| | - Jie Li
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Sayantani Nandi
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Hiu Fung Yuen
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Shu-Dong Zhang
- Northern Ireland Centre for Stratified Medicine, Ulster University, C-TRIC, Londonderry, United Kingdom
| | - Yeoh Khay Guan
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Jimmy So
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Division of Surgical Oncology (Upper Gastrointestinal Surgery), National University Cancer Institute, Singapore
| | - Qi Zeng
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore
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32
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Label-free cytokine micro- and nano-biosensing towards personalized medicine of systemic inflammatory disorders. Adv Drug Deliv Rev 2015; 95:90-103. [PMID: 26408791 DOI: 10.1016/j.addr.2015.09.005] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 08/17/2015] [Accepted: 09/10/2015] [Indexed: 01/31/2023]
Abstract
Systemic inflammatory disorders resulting from infection, trauma, surgery, and severe disease conditions pose serious threats to human health leading to organ dysfunction, organ failure, and mortality. The highly complex and dynamic nature of the immune system experiencing acute inflammation makes immunomodulatory therapy blocking pro-inflammatory cytokines very challenging. Successful therapy requires the ability to determine appropriate anti-cytokine drugs to be delivered at a right dose in a timely manner. Label-free micro- and nano-biosensors hold the potential to overcome the current challenges, enabling cytokine-targeted treatments to be tailored according to the immune status of an individual host with their unique cytokine biomarker detection capabilities. This review studies the recent progress in label-free cytokine biosensors, summarizes their performances and potential merits, and discusses future directions for their advancements to meet challenges towards personalized anti-cytokine drug delivery.
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33
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Solution Equilibrium Titration for High-Throughput Affinity Estimation of Unpurified Antibodies and Antibody Fragments. ACTA ACUST UNITED AC 2015; 20:1256-67. [DOI: 10.1177/1087057115595002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 06/14/2015] [Indexed: 01/14/2023]
Abstract
The generation of therapeutic antibodies with extremely high affinities down to the low picomolar range is today feasible with state-of-the art recombinant technologies. However, reliable and efficient identification of lead candidates with the desired affinity from a pool of thousands of antibody clones remains a challenge. Here, we describe a high-throughput procedure that allows reliable affinity screening of unpurified immunoglobulin G or antibody fragments. The method is based on the principle of solution equilibrium titration (SET) using highly sensitive electrochemiluminescence as a readout system. Because the binding partners are not labeled, the resulting KD represents a sound approximation of the real affinity. For screening, diluted bacterial lysates or cell culture supernatants are equilibrated with four different concentrations of a soluble target molecule, and unbound antibodies are subsequently quantified on 384-well Meso Scale Discovery (MSD) plates coated with the respective antigen. For determination of KD values from the resulting titration curves, fit models deduced from the law of mass action for 1:1 and 2:1 binding modes are applied to assess hundreds of interactions simultaneously. The accuracy of the method is demonstrated by comparing results from different screening campaigns from affinity optimization projects with results from detailed affinity characterization.
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34
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Kinetic Analyses of Data from a Human Serum Albumin Assay Using the liSPR System. BIOSENSORS-BASEL 2015; 5:27-36. [PMID: 25607476 PMCID: PMC4384080 DOI: 10.3390/bios5010027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Revised: 09/26/2014] [Accepted: 12/19/2014] [Indexed: 12/22/2022]
Abstract
We used the interaction between human serum albumin (HSA) and a high-affinity antibody to evaluate binding affinity measurements by the bench-top liSPR system (capitalis technology GmbH). HSA was immobilized directly onto a carboxylated sensor layer, and the mechanism of interaction between the antibody and HSA was investigated. The bivalence and heterogeneity of the antibody caused a complex binding mechanism. Three different interaction models (1:1 binding, heterogeneous analyte, bivalent analyte) were compared, and the bivalent analyte model best fit the curves obtained from the assay. This model describes the interaction of a bivalent analyte with one or two ligands (A + L ↔ LA + L ↔ LLA). The apparent binding affinity for this model measured 37 pM for the first reaction step, and 20 pM for the second step.
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35
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Davidoff SN, Ditto NT, Brooks AE, Eckman J, Brooks BD. Surface Plasmon Resonance for Therapeutic Antibody Characterization. ACTA ACUST UNITED AC 2015. [DOI: 10.1007/978-1-4939-2617-6_3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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36
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Bondza S, Stenberg J, Nestor M, Andersson K, Björkelund H. Conjugation Effects on Antibody–Drug Conjugates: Evaluation of Interaction Kinetics in Real Time on Living Cells. Mol Pharm 2014; 11:4154-63. [DOI: 10.1021/mp500379d] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Sina Bondza
- Section
of Biomedical Radiation Sciences, Department of Radiology, Oncology
and Radiation Science, Rudbeck Laboratory, Uppsala University, SE-751
85 Uppsala, Sweden
| | - Jonas Stenberg
- Section
of Biomedical Radiation Sciences, Department of Radiology, Oncology
and Radiation Science, Rudbeck Laboratory, Uppsala University, SE-751
85 Uppsala, Sweden
- Ridgeview Instruments AB, Vänge, Sweden
| | - Marika Nestor
- Section
of Biomedical Radiation Sciences, Department of Radiology, Oncology
and Radiation Science, Rudbeck Laboratory, Uppsala University, SE-751
85 Uppsala, Sweden
- Section
of Otolaryngology and Head and Neck Surgery, Department of Surgical
Sciences, Uppsala University, SE-751 85 Uppsala, Sweden
| | - Karl Andersson
- Section
of Biomedical Radiation Sciences, Department of Radiology, Oncology
and Radiation Science, Rudbeck Laboratory, Uppsala University, SE-751
85 Uppsala, Sweden
- Ridgeview Instruments AB, Vänge, Sweden
| | - Hanna Björkelund
- Section
of Biomedical Radiation Sciences, Department of Radiology, Oncology
and Radiation Science, Rudbeck Laboratory, Uppsala University, SE-751
85 Uppsala, Sweden
- Ridgeview Instruments AB, Vänge, Sweden
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37
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Yang J, Wang X, Fuh G, Yu L, Wakshull E, Khosraviani M, Day ES, Demeule B, Liu J, Shire SJ, Ferrara N, Yadav S. Comparison of binding characteristics and in vitro activities of three inhibitors of vascular endothelial growth factor A. Mol Pharm 2014; 11:3421-30. [PMID: 25162961 DOI: 10.1021/mp500160v] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The objectives of this study were to evaluate the relative binding and potencies of three inhibitors of vascular endothelial growth factor A (VEGF), used to treat neovascular age-related macular degeneration, and assess their relevance in the context of clinical outcome. Ranibizumab is a 48 kDa antigen binding fragment, which lacks a fragment crystallizable (Fc) region and is rapidly cleared from systemic circulation. Aflibercept, a 110 kDa fusion protein, and bevacizumab, a 150 kDa monoclonal antibody, each contain an Fc region. Binding affinities were determined using Biacore analysis. Competitive binding by sedimentation velocity analytical ultracentrifugation (SV-AUC) was used to support the binding affinities determined by Biacore of ranibizumab and aflibercept to VEGF. A bovine retinal microvascular endothelial cell (BREC) proliferation assay was used to measure potency. Biacore measurements were format dependent, especially for aflibercept, suggesting that biologically relevant, true affinities of recombinant VEGF (rhVEGF) and its inhibitors are yet to be determined. Despite this assay format dependency, ranibizumab appeared to be a very tight VEGF binder in all three formats. The results are also very comparable to those reported previously.1-3 At equivalent molar ratios, ranibizumab was able to displace aflibercept from preformed aflibercept/VEGF complexes in solution as assessed by SV-AUC, whereas aflibercept was not able to significantly displace ranibizumab from preformed ranibizumab/VEGF complexes. Ranibizumab, aflibercept, and bevacizumab showed dose-dependent inhibition of BREC proliferation induced by 6 ng/mL VEGF, with average IC50 values of 0.088 ± 0.032, 0.090 ± 0.009, and 0.500 ± 0.091 nM, respectively. Similar results were obtained with 3 ng/mL VEGF. In summary Biacore studies and SV-AUC solution studies show that aflibercept does not bind with higher affinity than ranibizumab to VEGF as recently reported,4 and both inhibitors appeared to be equipotent with respect to their ability to inhibit VEGF function.
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Affiliation(s)
- Jihong Yang
- Genentech, Inc. , 1 DNA Way, MS 56-2A, South San Francisco, California 94080, United States
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Mitchell T, Chao G, Sitkoff D, Lo F, Monshizadegan H, Meyers D, Low S, Russo K, DiBella R, Denhez F, Gao M, Myers J, Duke G, Witmer M, Miao B, Ho SP, Khan J, Parker RA. Pharmacologic profile of the Adnectin BMS-962476, a small protein biologic alternative to PCSK9 antibodies for low-density lipoprotein lowering. J Pharmacol Exp Ther 2014; 350:412-24. [PMID: 24917546 DOI: 10.1124/jpet.114.214221] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Proprotein convertase subtilisin kexin-9 (PCSK9) is an important pharmacological target for decreasing low-density lipoprotein (LDL) in cardiovascular disease, although seemingly inaccessible to small molecule approaches. Compared with therapeutic IgG antibodies currently in development, targeting circulating PCSK9 with smaller molecular scaffolds could offer different profiles and reduced dose burdens. This inspired genesis of PCSK9-binding Adnectins, a protein family derived from human fibronectin-10th-type III-domain and engineered for high-affinity target binding. BMS-962476, an ∼11-kDa polypeptide conjugated to polyethylene glycol to enhance pharmacokinetics, binds with subnanomolar affinity to human. The X-ray cocrystal structure of PCSK9 with a progenitor Adnectin shows ∼910 Å(2) of PCSK9 surface covered next to the LDL receptor binding site, largely by residues of a single loop of the Adnectin. In hypercholesterolemic, overexpressing human PCSK9 transgenic mice, BMS-962476 rapidly lowered cholesterol and free PCSK9 levels. In genomic transgenic mice, BMS-962476 potently reduced free human PCSK9 (ED50 ∼0.01 mg/kg) followed by ∼2-fold increases in total PCSK9 before return to baseline. Treatment of cynomolgus monkeys with BMS-962476 rapidly suppressed free PCSK9 >99% and LDL-cholesterol ∼55% with subsequent 6-fold increase in total PCSK9, suggesting reduced clearance of circulating complex. Liver sterol response genes were consequently downregulated, following which LDL and total PCSK9 returned to baseline. These studies highlight the rapid dynamics of PCSK9 control over LDL and liver cholesterol metabolism and characterize BMS-962476 as a potent and efficacious PCSK9 inhibitor.
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Affiliation(s)
- Tracy Mitchell
- Molecular Discovery Technologies (T.M., G.C., D.S., S.L., K.R., R.D., F.D., M.G., J.M., G.D., M.W., J.K.), Applied Genomics (S.P.H.), and Cardiovascular Discovery Biology (F.L., H.M., D.M., B.M., R.A.P.), Bristol-Myers Squibb Research and Development, Princeton, New Jersey
| | - Ginger Chao
- Molecular Discovery Technologies (T.M., G.C., D.S., S.L., K.R., R.D., F.D., M.G., J.M., G.D., M.W., J.K.), Applied Genomics (S.P.H.), and Cardiovascular Discovery Biology (F.L., H.M., D.M., B.M., R.A.P.), Bristol-Myers Squibb Research and Development, Princeton, New Jersey
| | - Doree Sitkoff
- Molecular Discovery Technologies (T.M., G.C., D.S., S.L., K.R., R.D., F.D., M.G., J.M., G.D., M.W., J.K.), Applied Genomics (S.P.H.), and Cardiovascular Discovery Biology (F.L., H.M., D.M., B.M., R.A.P.), Bristol-Myers Squibb Research and Development, Princeton, New Jersey
| | - Fred Lo
- Molecular Discovery Technologies (T.M., G.C., D.S., S.L., K.R., R.D., F.D., M.G., J.M., G.D., M.W., J.K.), Applied Genomics (S.P.H.), and Cardiovascular Discovery Biology (F.L., H.M., D.M., B.M., R.A.P.), Bristol-Myers Squibb Research and Development, Princeton, New Jersey
| | - Hossain Monshizadegan
- Molecular Discovery Technologies (T.M., G.C., D.S., S.L., K.R., R.D., F.D., M.G., J.M., G.D., M.W., J.K.), Applied Genomics (S.P.H.), and Cardiovascular Discovery Biology (F.L., H.M., D.M., B.M., R.A.P.), Bristol-Myers Squibb Research and Development, Princeton, New Jersey
| | - Daniel Meyers
- Molecular Discovery Technologies (T.M., G.C., D.S., S.L., K.R., R.D., F.D., M.G., J.M., G.D., M.W., J.K.), Applied Genomics (S.P.H.), and Cardiovascular Discovery Biology (F.L., H.M., D.M., B.M., R.A.P.), Bristol-Myers Squibb Research and Development, Princeton, New Jersey
| | - Simon Low
- Molecular Discovery Technologies (T.M., G.C., D.S., S.L., K.R., R.D., F.D., M.G., J.M., G.D., M.W., J.K.), Applied Genomics (S.P.H.), and Cardiovascular Discovery Biology (F.L., H.M., D.M., B.M., R.A.P.), Bristol-Myers Squibb Research and Development, Princeton, New Jersey
| | - Katie Russo
- Molecular Discovery Technologies (T.M., G.C., D.S., S.L., K.R., R.D., F.D., M.G., J.M., G.D., M.W., J.K.), Applied Genomics (S.P.H.), and Cardiovascular Discovery Biology (F.L., H.M., D.M., B.M., R.A.P.), Bristol-Myers Squibb Research and Development, Princeton, New Jersey
| | - Rose DiBella
- Molecular Discovery Technologies (T.M., G.C., D.S., S.L., K.R., R.D., F.D., M.G., J.M., G.D., M.W., J.K.), Applied Genomics (S.P.H.), and Cardiovascular Discovery Biology (F.L., H.M., D.M., B.M., R.A.P.), Bristol-Myers Squibb Research and Development, Princeton, New Jersey
| | - Fabienne Denhez
- Molecular Discovery Technologies (T.M., G.C., D.S., S.L., K.R., R.D., F.D., M.G., J.M., G.D., M.W., J.K.), Applied Genomics (S.P.H.), and Cardiovascular Discovery Biology (F.L., H.M., D.M., B.M., R.A.P.), Bristol-Myers Squibb Research and Development, Princeton, New Jersey
| | - Mian Gao
- Molecular Discovery Technologies (T.M., G.C., D.S., S.L., K.R., R.D., F.D., M.G., J.M., G.D., M.W., J.K.), Applied Genomics (S.P.H.), and Cardiovascular Discovery Biology (F.L., H.M., D.M., B.M., R.A.P.), Bristol-Myers Squibb Research and Development, Princeton, New Jersey
| | - Joseph Myers
- Molecular Discovery Technologies (T.M., G.C., D.S., S.L., K.R., R.D., F.D., M.G., J.M., G.D., M.W., J.K.), Applied Genomics (S.P.H.), and Cardiovascular Discovery Biology (F.L., H.M., D.M., B.M., R.A.P.), Bristol-Myers Squibb Research and Development, Princeton, New Jersey
| | - Gerald Duke
- Molecular Discovery Technologies (T.M., G.C., D.S., S.L., K.R., R.D., F.D., M.G., J.M., G.D., M.W., J.K.), Applied Genomics (S.P.H.), and Cardiovascular Discovery Biology (F.L., H.M., D.M., B.M., R.A.P.), Bristol-Myers Squibb Research and Development, Princeton, New Jersey
| | - Mark Witmer
- Molecular Discovery Technologies (T.M., G.C., D.S., S.L., K.R., R.D., F.D., M.G., J.M., G.D., M.W., J.K.), Applied Genomics (S.P.H.), and Cardiovascular Discovery Biology (F.L., H.M., D.M., B.M., R.A.P.), Bristol-Myers Squibb Research and Development, Princeton, New Jersey
| | - Bowman Miao
- Molecular Discovery Technologies (T.M., G.C., D.S., S.L., K.R., R.D., F.D., M.G., J.M., G.D., M.W., J.K.), Applied Genomics (S.P.H.), and Cardiovascular Discovery Biology (F.L., H.M., D.M., B.M., R.A.P.), Bristol-Myers Squibb Research and Development, Princeton, New Jersey
| | - Siew P Ho
- Molecular Discovery Technologies (T.M., G.C., D.S., S.L., K.R., R.D., F.D., M.G., J.M., G.D., M.W., J.K.), Applied Genomics (S.P.H.), and Cardiovascular Discovery Biology (F.L., H.M., D.M., B.M., R.A.P.), Bristol-Myers Squibb Research and Development, Princeton, New Jersey
| | - Javed Khan
- Molecular Discovery Technologies (T.M., G.C., D.S., S.L., K.R., R.D., F.D., M.G., J.M., G.D., M.W., J.K.), Applied Genomics (S.P.H.), and Cardiovascular Discovery Biology (F.L., H.M., D.M., B.M., R.A.P.), Bristol-Myers Squibb Research and Development, Princeton, New Jersey
| | - Rex A Parker
- Molecular Discovery Technologies (T.M., G.C., D.S., S.L., K.R., R.D., F.D., M.G., J.M., G.D., M.W., J.K.), Applied Genomics (S.P.H.), and Cardiovascular Discovery Biology (F.L., H.M., D.M., B.M., R.A.P.), Bristol-Myers Squibb Research and Development, Princeton, New Jersey
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39
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Fechner P, Bleher O, Ewald M, Freudenberger K, Furin D, Hilbig U, Kolarov F, Krieg K, Leidner L, Markovic G, Proll G, Pröll F, Rau S, Riedt J, Schwarz B, Weber P, Widmaier J. Size does matter! Label-free detection of small molecule-protein interaction. Anal Bioanal Chem 2014; 406:4033-51. [PMID: 24817356 DOI: 10.1007/s00216-014-7834-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 04/07/2014] [Accepted: 04/11/2014] [Indexed: 11/28/2022]
Abstract
This review is focused on methods for detecting small molecules and, in particular, the characterisation of their interaction with natural proteins (e.g. receptors, ion channels). Because there are intrinsic advantages to using label-free methods over labelled methods (e.g. fluorescence, radioactivity), this review only covers label-free techniques. We briefly discuss available techniques and their advantages and disadvantages, especially as related to investigating the interaction between small molecules and proteins. The reviewed techniques include well-known and widely used standard analytical methods (e.g. HPLC-MS, NMR, calorimetry, and X-ray diffraction), newer and more specialised analytical methods (e.g. biosensors), biological systems (e.g. cell lines and animal models), and in-silico approaches.
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Affiliation(s)
- Peter Fechner
- Biametrics GmbH, Auf der Morgenstelle 18, 72076, Tübingen, Germany,
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40
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Barta P, Andersson K, Trejtnar F, Buijs J. Exploring Time-Resolved Characterization of the Heterogeneity and Dynamics of Ligand-Receptor Interactions on Living Cells. ACTA ACUST UNITED AC 2014. [DOI: 10.6000/1927-7229.2014.03.02.4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
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Abstract
ABSTRACT
Advanced molecular biology techniques developed during the past few decades have allowed the industry to exploit and commercialize the natural defense mechanisms that antibodies provide. This review discusses the latest advances in antibody-engineering technologies to enhance clinical efficacy and outcomes. For the constant regions, the choice of the antibody class and isotype has to be made carefully to suit the therapeutic applications. Engineering of the Fc region, either by direct targeted mutagenesis or by modifying the nature of its
N
-glycan, has played an important role in recent years in increasing half-life or controlling effector functions. The variable regions of the antibody are responsible for binding affinity and exquisite specificity to the target molecule, which together with the Fc determine the drug's efficacy and influence the drug dose required to obtain the desired effectiveness. A key requirement during antibody development is therefore to affinity mature the variable regions when necessary, so that they bind the therapeutic target with sufficiently high affinity to guarantee effective occupancy over prolonged periods. If the antibody was obtained from a non-human source, such as rodents, a humanization process has to be applied to minimize immunogenicity while maintaining the desired binding affinity and selectivity. Finally, we discuss the next next-generation antibodies, such as antibody-drug conjugates, bispecific antibodies, and immunocytokines, which are being developed to meet future challenges.
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Bee C, Abdiche YN, Pons J, Rajpal A. Determining the binding affinity of therapeutic monoclonal antibodies towards their native unpurified antigens in human serum. PLoS One 2013; 8:e80501. [PMID: 24223227 PMCID: PMC3819287 DOI: 10.1371/journal.pone.0080501] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Accepted: 10/03/2013] [Indexed: 02/02/2023] Open
Abstract
Monoclonal antibodies (mAbs) are a growing segment of therapeutics, yet their in vitro characterization remains challenging. While it is essential that a therapeutic mAb recognizes the native, physiologically occurring epitope, the generation and selection of mAbs often rely on the use of purified recombinant versions of the antigen that may display non-native epitopes. Here, we present a method to measure both, the binding affinity of a therapeutic mAb towards its native unpurified antigen in human serum, and the antigen’s endogenous concentration, by combining the kinetic exclusion assay and Biacore’s calibration free concentration analysis. To illustrate the broad utility of our method, we studied a panel of mAbs raised against three disparate soluble antigens that are abundant in the serum of healthy donors: proprotein convertase subtilisin/kexin type 9 (PCSK9), progranulin (PGRN), and fatty acid binding protein (FABP4). We also determined the affinity of each mAb towards its purified recombinant antigen and assessed whether the interactions were pH-dependent. Of the six mAbs studied, three did not appear to discriminate between the serum and recombinant forms of the antigen; one mAb bound serum antigen with a higher affinity than recombinant antigen; and two mAbs displayed a different affinity for serum antigen that could be explained by a pH-dependent interaction. Our results highlight the importance of taking pH into account when measuring the affinities of mAbs towards their serum antigens, since the pH of serum samples becomes increasingly alkaline upon aerobic handling.
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Affiliation(s)
- Christine Bee
- Rinat, Pfizer Inc., South San Francisco, California, United States of America
| | - Yasmina N. Abdiche
- Rinat, Pfizer Inc., South San Francisco, California, United States of America
- * E-mail:
| | - Jaume Pons
- Rinat, Pfizer Inc., South San Francisco, California, United States of America
| | - Arvind Rajpal
- Rinat, Pfizer Inc., South San Francisco, California, United States of America
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43
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Allowance for antibody bivalence in the determination of association rate constants by kinetic exclusion assay. Anal Biochem 2013; 441:214-7. [DOI: 10.1016/j.ab.2013.06.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Revised: 06/22/2013] [Accepted: 06/24/2013] [Indexed: 11/18/2022]
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44
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Rebhan MAE, Brunschweiger A, Hall J. Measurement by SPR of Very Low Dissociation Rates: Oxidation-Mediated Loss of Biotin-Streptavidin Affinity. Chembiochem 2013; 14:2091-4. [DOI: 10.1002/cbic.201300468] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Indexed: 12/17/2022]
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45
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Giavazzi F, Salina M, Cerbino R, Bassi M, Prosperi D, Ceccarello E, Damin F, Sola L, Rusnati M, Chiari M, Chini B, Bellini T, Buscaglia M. Multispot, label-free biodetection at a phantom plastic-water interface. Proc Natl Acad Sci U S A 2013; 110:9350-5. [PMID: 23696673 PMCID: PMC3677498 DOI: 10.1073/pnas.1214589110] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Recognizing and quantifying specific biomolecules in aqueous samples are constantly needed in research and diagnostic laboratories. As the typical detection procedures are rather lengthy and involve the use of labeled secondary antibodies or other agents to provide a signal, efforts have been made over the last 10 y to develop alternative label-free methods that enable direct detection. We propose and demonstrate an extremely simple, low-cost, label-free biodetector based on measuring the intensity of light reflected by the interface between a fluid sample and an amorphous fluoropolymer substrate having a refractive index very close to that of water and hosting various antibodies immobilized in spots. Under these index-matching conditions, the amount of light reflected by the interface allows straightforward quantification of the amount of antigen binding to each spot. Using antibodies targeting heterologous immunoglobulins and antigens commonly used as markers for diagnoses of hepatitis B and HIV, we demonstrate the limit of detection of a few picograms per square millimeter of surface-bound molecules. We also show that direct and real-time access to the amount of binding molecules allows the precise extrapolation of adhesion rates, from which the concentrations of antigens in solution can be estimated down to fractions of nanograms per milliliter.
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Affiliation(s)
- Fabio Giavazzi
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, 20090 Segrate, Italy
- Proxentia S.r.l., 20135 Milan, Italy
| | - Matteo Salina
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, 20090 Segrate, Italy
- Proxentia S.r.l., 20135 Milan, Italy
| | - Roberto Cerbino
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, 20090 Segrate, Italy
| | - Mattia Bassi
- Materials Science Department, Solvay Specialty Polymers Research and Development Center, 20021 Bollate, Italy
| | - Davide Prosperi
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano-Bicocca, 20126 Milan, Italy
| | - Erica Ceccarello
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, 20090 Segrate, Italy
- Proxentia S.r.l., 20135 Milan, Italy
| | - Francesco Damin
- Istituto di Chimica del Riconoscimento Molecolare–Consiglio Nazionale delle Ricerche, 20131 Milan, Italy
| | - Laura Sola
- Istituto di Chimica del Riconoscimento Molecolare–Consiglio Nazionale delle Ricerche, 20131 Milan, Italy
| | - Marco Rusnati
- Dipartimento di Medicina Molecolare e Traslazionale, Università degli Studi di Brescia, 25123 Brescia, Italy; and
| | - Marcella Chiari
- Istituto di Chimica del Riconoscimento Molecolare–Consiglio Nazionale delle Ricerche, 20131 Milan, Italy
| | - Bice Chini
- Istituto di Neuroscienze–Consiglio Nazionale delle Ricerche, 20129 Milan, Italy
| | - Tommaso Bellini
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, 20090 Segrate, Italy
| | - Marco Buscaglia
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, 20090 Segrate, Italy
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Rispens T, Heer POD, Derksen NI, Wolbink G, van Schouwenburg PA, Kruithof S, Aalberse RC. Nanomolar to sub-picomolar affinity measurements of antibody–antigen interactions and protein multimerizations: Fluorescence-assisted high-performance liquid chromatography. Anal Biochem 2013; 437:118-22. [DOI: 10.1016/j.ab.2013.02.027] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Revised: 02/24/2013] [Accepted: 02/26/2013] [Indexed: 01/01/2023]
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47
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Day ES, Capili AD, Borysenko CW, Zafari M, Whitty A. Determining the affinity and stoichiometry of interactions between unmodified proteins in solution using Biacore. Anal Biochem 2013; 440:96-107. [PMID: 23711722 DOI: 10.1016/j.ab.2013.05.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Revised: 05/03/2013] [Accepted: 05/10/2013] [Indexed: 11/30/2022]
Abstract
We describe a general Biacore method for measuring equilibrium binding affinities and stoichiometries for interactions between unmodified proteins and their unmodified ligands free in solution. Mixtures of protein and ligand are preequilibrated at different ratios in solution and then analyzed by Biacore using a sensor chip surface that detects only unbound analyte. Performing the Biacore analysis under mass transport limited conditions allows the concentration of unbound analyte to be determined from the initial velocity of binding. Plots of initial velocity versus the concentration of the varied binding partner are fitted to a quadratic binding equation to give the affinity and stoichiometry of binding. We demonstrate the method using soluble Her2 extracellular domain binding to monovalent, bivalent, and trivalent forms of an anti-Her2 antibody. The affinity we measured agrees with that obtained from conventional Biacore kinetic analysis, and the stoichiometries for the resulting 1:1, 1:2, and 1:3 complexes were confirmed by gel filtration with in-line light scattering. The method is applicable over an affinity range of approximately 100 pM to 1 μM and is particularly useful when there is concern that covalently modifying one or the other binding partner might affect its binding properties or where multivalency might otherwise complicate a quantitative analysis of binding.
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Papadopoulos N, Martin J, Ruan Q, Rafique A, Rosconi MP, Shi E, Pyles EA, Yancopoulos GD, Stahl N, Wiegand SJ. Binding and neutralization of vascular endothelial growth factor (VEGF) and related ligands by VEGF Trap, ranibizumab and bevacizumab. Angiogenesis 2012; 15:171-85. [PMID: 22302382 PMCID: PMC3338918 DOI: 10.1007/s10456-011-9249-6] [Citation(s) in RCA: 762] [Impact Index Per Article: 63.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2011] [Accepted: 12/17/2011] [Indexed: 12/27/2022]
Abstract
Pharmacological inhibition of VEGF-A has proven to be effective in inhibiting angiogenesis and vascular leak associated with cancers and various eye diseases. However, little information is currently available on the binding kinetics and relative biological activity of various VEGF inhibitors. Therefore, we have evaluated the binding kinetics of two anti-VEGF antibodies, ranibizumab and bevacizumab, and VEGF Trap (also known as aflibercept), a novel type of soluble decoy receptor, with substantially higher affinity than conventional soluble VEGF receptors. VEGF Trap bound to all isoforms of human VEGF-A tested with subpicomolar affinity. Ranibizumab and bevacizumab also bound human VEGF-A, but with markedly lower affinity. The association rate for VEGF Trap binding to VEGF-A was orders of magnitude faster than that measured for bevacizumab and ranibizumab. Similarly, in cell-based bioassays, VEGF Trap inhibited the activation of VEGFR1 and VEGFR2, as well as VEGF-A induced calcium mobilization and migration in human endothelial cells more potently than ranibizumab or bevacizumab. Only VEGF Trap bound human PlGF and VEGF-B, and inhibited VEGFR1 activation and HUVEC migration induced by PlGF. These data differentiate VEGF Trap from ranibizumab and bevacizumab in terms of its markedly higher affinity for VEGF-A, as well as its ability to bind VEGF-B and PlGF.
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49
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High-affinity target binding engineered via fusion of a single-domain antibody fragment with a ligand-tailored SH3 domain. PLoS One 2012; 7:e40331. [PMID: 22792285 PMCID: PMC3390362 DOI: 10.1371/journal.pone.0040331] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2012] [Accepted: 06/05/2012] [Indexed: 11/19/2022] Open
Abstract
Monoclonal and recombinant antibodies are ubiquitous tools in diagnostics, therapeutics, and biotechnology. However, their biochemical properties lack optimal robustness, their bacterial production is not easy, and possibilities to create multifunctional fusion proteins based on them are limited. Moreover, the binding affinities of antibodies towards their antigens are suboptimal for many applications where they are commonly used. To address these issues we have made use of the concept of creating high binding affinity based on multivalent target recognition via exploiting some of the best features of immunoglobulins (Ig) and non-Ig-derived ligand-binding domains. We have constructed a small protein, named Neffin, comprised of a 118 aa llama Ig heavy chain variable domain fragment (VHH) fused to a ligand-tailored 57 aa SH3 domain. Neffin could be readily produced in large amounts (>18 mg/L) in the cytoplasm of E. coli, and bound with a subpicomolar affinity (Kd 0.54 pM) to its target, the HIV-1 Nef protein. When expressed in human cells Neffin could potently inhibit Nef function. Similar VHH-SH3 fusion proteins could be targeted against many other proteins of interest and could have widespread use in diverse medical and biotechnology applications where biochemical robustness and strong binding affinity are required.
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50
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Drake AW, Tang ML, Papalia GA, Landes G, Haak-Frendscho M, Klakamp SL. Biacore surface matrix effects on the binding kinetics and affinity of an antigen/antibody complex. Anal Biochem 2012; 429:58-69. [PMID: 22766435 DOI: 10.1016/j.ab.2012.06.024] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2012] [Revised: 06/20/2012] [Accepted: 06/25/2012] [Indexed: 12/15/2022]
Abstract
To characterize a proprietary therapeutic monoclonal antibody (mAb) candidate, a rigorous biophysical study consisting of 53 Biacore and kinetic exclusion assay (KinExA) experiments was undertaken on the therapeutic mAb complexing with its target antigen. Unexpectedly, the observed binding kinetics depended on the chip used, suggesting that the negatively charged carboxyl groups on CM5, CM4, and C1 chips were adversely affecting the Biacore kinetic results. To study this hypothesis, Biacore solution-phase and KinExA equilibrium titrations, as well as KinExA kinetic measurements, were performed to establish accurate values for the affinity and kinetic rate constants of the binding reaction between antigen and mAb. The results revealed that as the negative charge on the biosensor surface decreased, the binding kinetics and K(D) approached the accurate binding parameters more closely when measured in solution. Two potential causes for the artifactual Biacore surface-based measurements are (i) steric hindrance of antigen binding arising from an interaction of the negatively charged carboxymethyldextran matrix with the mAb, which is a highly basic protein with a pI of 9.4, and (ii) an electrostatic repulsion between the negatively charged antigen and the carboxymethyldextran matrix. Importantly, simple diagnostic tests can be performed early in the measurement process to identify these types of matrix-mediated artifacts.
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Affiliation(s)
- Andrew W Drake
- Takeda San Francisco, 285 E. Grand Ave. South San Francisco, CA 94080, USA
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