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Qian L, Lin X, Gao X, Khan RU, Liao JY, Du S, Ge J, Zeng S, Yao SQ. The Dawn of a New Era: Targeting the "Undruggables" with Antibody-Based Therapeutics. Chem Rev 2023. [PMID: 37186942 DOI: 10.1021/acs.chemrev.2c00915] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
The high selectivity and affinity of antibodies toward their antigens have made them a highly valuable tool in disease therapy, diagnosis, and basic research. A plethora of chemical and genetic approaches have been devised to make antibodies accessible to more "undruggable" targets and equipped with new functions of illustrating or regulating biological processes more precisely. In this Review, in addition to introducing how naked antibodies and various antibody conjugates (such as antibody-drug conjugates, antibody-oligonucleotide conjugates, antibody-enzyme conjugates, etc.) work in therapeutic applications, special attention has been paid to how chemistry tools have helped to optimize the therapeutic outcome (i.e., with enhanced efficacy and reduced side effects) or facilitate the multifunctionalization of antibodies, with a focus on emerging fields such as targeted protein degradation, real-time live-cell imaging, catalytic labeling or decaging with spatiotemporal control as well as the engagement of antibodies inside cells. With advances in modern chemistry and biotechnology, well-designed antibodies and their derivatives via size miniaturization or multifunctionalization together with efficient delivery systems have emerged, which have gradually improved our understanding of important biological processes and paved the way to pursue novel targets for potential treatments of various diseases.
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Affiliation(s)
- Linghui Qian
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Cancer Center, & Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou 310058, China
| | - Xuefen Lin
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Cancer Center, & Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou 310058, China
| | - Xue Gao
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Cancer Center, & Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou 310058, China
| | - Rizwan Ullah Khan
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Cancer Center, & Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou 310058, China
| | - Jia-Yu Liao
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Cancer Center, & Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou 310058, China
| | - Shubo Du
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Jingyan Ge
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Su Zeng
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Cancer Center, & Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou 310058, China
| | - Shao Q Yao
- Department of Chemistry, National University of Singapore, 4 Science Drive 2, Singapore, 117544
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O'Byrne PM, Panettieri RA, Taube C, Brindicci C, Fleming M, Altman P. Development of an inhaled anti-TSLP therapy for asthma. Pulm Pharmacol Ther 2023; 78:102184. [PMID: 36535465 DOI: 10.1016/j.pupt.2022.102184] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 11/24/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022]
Abstract
Thymic stromal lymphopoietin (TSLP), an epithelial cell-derived cytokine, acts as a key mediator in airway inflammation and modulates the function of multiple cell types, including dendritic cells and group 2 innate lymphoid cells. TSLP plays a role in asthma pathogenesis as an upstream cytokine, and data suggest that TSLP blockade with the anti-TSLP monoclonal antibody, tezepelumab, could be efficacious in a broad asthma population. Currently approved asthma biologic therapies target allergic or eosinophilic disease and require phenotyping; therefore, an unmet need exists for a therapy that can address Type 2 (T2)-high and T2-low inflammation in asthma. All currently approved biologic treatments are delivered intravenously or subcutaneously; an inhaled therapy route that allows direct targeting of the lung with reduced systemic impact may offer advantages. Currently in development, ecleralimab (CSJ117) represents the first inhaled anti-TSLP antibody fragment that binds soluble TSLP and prevents TSLP receptor activation, thereby inhibiting further inflammatory signalling cascades. This anti-TSLP antibody fragment is being developed for patients with severe uncontrolled asthma despite standard of care inhaled therapy. A Phase IIa proof of concept study, using allergen bronchoprovocation as a model for asthma exacerbations, found that ecleralimab was well-tolerated and reduced allergen-induced bronchoconstriction in adult patients with mild asthma. These results suggest ecleralimab may be a promising, new therapeutic class for asthma treatment.
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Affiliation(s)
- Paul M O'Byrne
- Firestone Institute for Respiratory Health, St. Joseph's Healthcare and McMaster University, Hamilton, Ontario, Canada.
| | | | - Christian Taube
- Department of Pulmonary Medicine, University Hospital Essen, Germany
| | | | | | - Pablo Altman
- Novartis Pharmaceuticals Corporation, New Jersey, USA.
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3
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Site-Specific Antibody Conjugation with Payloads beyond Cytotoxins. Molecules 2023; 28:molecules28030917. [PMID: 36770585 PMCID: PMC9921355 DOI: 10.3390/molecules28030917] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 01/12/2023] [Accepted: 01/15/2023] [Indexed: 01/18/2023] Open
Abstract
As antibody-drug conjugates have become a very important modality for cancer therapy, many site-specific conjugation approaches have been developed for generating homogenous molecules. The selective antibody coupling is achieved through antibody engineering by introducing specific amino acid or unnatural amino acid residues, peptides, and glycans. In addition to the use of synthetic cytotoxins, these novel methods have been applied for the conjugation of other payloads, including non-cytotoxic compounds, proteins/peptides, glycans, lipids, and nucleic acids. The non-cytotoxic compounds include polyethylene glycol, antibiotics, protein degraders (PROTAC and LYTAC), immunomodulating agents, enzyme inhibitors and protein ligands. Different small proteins or peptides have been selectively conjugated through unnatural amino acid using click chemistry, engineered C-terminal formylglycine for oxime or click chemistry, or specific ligation or transpeptidation with or without enzymes. Although the antibody protamine peptide fusions have been extensively used for siRNA coupling during early studies, direct conjugations through engineered cysteine or lysine residues have been demonstrated later. These site-specific antibody conjugates containing these payloads other than cytotoxic compounds can be used in proof-of-concept studies and in developing new therapeutics for unmet medical needs.
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Morris NM, Blee JA, Hauert S. Developing a computational pharmacokinetic model of systemic snakebite envenomation and antivenom treatment. Toxicon 2022; 215:77-90. [PMID: 35716719 DOI: 10.1016/j.toxicon.2022.06.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 05/20/2022] [Accepted: 06/09/2022] [Indexed: 11/19/2022]
Abstract
Snakebite envenomation is responsible for over 100,000 deaths and 400,000 cases of disability annually, most of which are preventable through access to safe and effective antivenoms. Snake venom toxins span a wide molecular weight range, influencing their absorption, distribution, and elimination within the body. In recent years, a range of scaffolds have been applied to antivenom development. These scaffolds similarly span a wide molecular weight range and subsequently display diverse pharmacokinetic behaviours. Computational simulations represent a powerful tool to explore the interplay between these varied antivenom scaffolds and venoms, to assess whether a pharmacokinetically optimal antivenom exists. The purpose of this study was to establish a computational model of systemic snakebite envenomation and treatment, for the quantitative assessment and comparison of conventional and next-generation antivenoms. A two-compartment mathematical model of envenomation and treatment was defined and the system was parameterised using existing data from rabbits. Elimination and biodistribution parameters were regressed against molecular weight to predict the dynamics of IgG, F(ab')2, Fab, scFv, and nanobody antivenoms, spanning a size range of 15-150 kDa. As a case study, intramuscular envenomation by Naja sumatrana (equatorial spitting cobra) and its treatment using Fab, F(ab')2, and IgG antivenoms was simulated. Variable venom dose tests were applied to visualise effective antivenom dose levels. Comparisons to existing antivenoms and experimental rescue studies highlight the large dose reductions that could result from recombinant antivenom use. This study represents the first comparative in silico model of snakebite envenomation and treatment.
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Affiliation(s)
- Natalie M Morris
- Department of Engineering Mathematics, Ada Lovelace Building, University of Bristol, University Walk, Bristol, BS8 1TW, UK.
| | - Johanna A Blee
- Department of Engineering Mathematics, Ada Lovelace Building, University of Bristol, University Walk, Bristol, BS8 1TW, UK.
| | - Sabine Hauert
- Department of Engineering Mathematics, Ada Lovelace Building, University of Bristol, University Walk, Bristol, BS8 1TW, UK.
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Walles M, Berna MJ, Jian W, Hauri S, Hengel S, King L, Tran JC, Wei C, Xu K, Zhu X. A Cross Company Perspective on the Assessment of Therapeutic Protein Biotransformation. Drug Metab Dispos 2022; 50:846-857. [DOI: 10.1124/dmd.121.000462] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 03/02/2022] [Indexed: 11/22/2022] Open
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Sandomenico A, Sivaccumar JP, Ruvo M. Evolution of Escherichia coli Expression System in Producing Antibody Recombinant Fragments. Int J Mol Sci 2020; 21:ijms21176324. [PMID: 32878291 PMCID: PMC7504322 DOI: 10.3390/ijms21176324] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 08/12/2020] [Accepted: 08/25/2020] [Indexed: 02/07/2023] Open
Abstract
Antibodies and antibody-derived molecules are continuously developed as both therapeutic agents and key reagents for advanced diagnostic investigations. Their application in these fields has indeed greatly expanded the demand of these molecules and the need for their production in high yield and purity. While full-length antibodies require mammalian expression systems due to the occurrence of functionally and structurally important glycosylations, most antibody fragments and antibody-like molecules are non-glycosylated and can be more conveniently prepared in E. coli-based expression platforms. We propose here an updated survey of the most effective and appropriate methods of preparation of antibody fragments that exploit E. coli as an expression background and review the pros and cons of the different platforms available today. Around 250 references accompany and complete the review together with some lists of the most important new antibody-like molecules that are on the market or are being developed as new biotherapeutics or diagnostic agents.
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Moncalvo F, Martinez Espinoza MI, Cellesi F. Nanosized Delivery Systems for Therapeutic Proteins: Clinically Validated Technologies and Advanced Development Strategies. Front Bioeng Biotechnol 2020; 8:89. [PMID: 32117952 PMCID: PMC7033645 DOI: 10.3389/fbioe.2020.00089] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 01/30/2020] [Indexed: 12/18/2022] Open
Abstract
The impact of protein therapeutics in healthcare is steadily increasing, due to advancements in the field of biotechnology and a deeper understanding of several pathologies. However, their safety and efficacy are often limited by instability, short half-life and immunogenicity. Nanodelivery systems are currently being investigated for overcoming these limitations and include covalent attachment of biocompatible polymers (PEG and other synthetic or naturally derived macromolecules) as well as protein nanoencapsulation in colloidal systems (liposomes and other lipid or polymeric nanocarriers). Such strategies have the potential to develop next-generation protein therapeutics. Herein, we review recent research progresses on these nanodelivery approaches, as well as future directions and challenges.
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Affiliation(s)
| | | | - Francesco Cellesi
- Dipartimento di Chimica, Materiali e Ingegneria Chimica “G. Natta”, Politecnico di Milano, Milan, Italy
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Raybould MIJ, Marks C, Lewis AP, Shi J, Bujotzek A, Taddese B, Deane CM. Thera-SAbDab: the Therapeutic Structural Antibody Database. Nucleic Acids Res 2020; 48:D383-D388. [PMID: 31555805 PMCID: PMC6943036 DOI: 10.1093/nar/gkz827] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 09/09/2019] [Accepted: 09/24/2019] [Indexed: 12/17/2022] Open
Abstract
The Therapeutic Structural Antibody Database (Thera-SAbDab; http://opig.stats.ox.ac.uk/webapps/therasabdab) tracks all antibody- and nanobody-related therapeutics recognized by the World Health Organisation (WHO), and identifies any corresponding structures in the Structural Antibody Database (SAbDab) with near-exact or exact variable domain sequence matches. Thera-SAbDab is synchronized with SAbDab to update weekly, reflecting new Protein Data Bank entries and the availability of new sequence data published by the WHO. Each therapeutic summary page lists structural coverage (with links to the appropriate SAbDab entries), alignments showing where any near-matches deviate in sequence, and accompanying metadata, such as intended target and investigated conditions. Thera-SAbDab can be queried by therapeutic name, by a combination of metadata, or by variable domain sequence - returning all therapeutics that are within a specified sequence identity over a specified region of the query. The sequences of all therapeutics listed in Thera-SAbDab (461 unique molecules, as of 5 August 2019) are downloadable as a single file with accompanying metadata.
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Affiliation(s)
- Matthew I J Raybould
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, 24-29 St Giles’, Oxford OX1 3LB, UK
| | - Claire Marks
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, 24-29 St Giles’, Oxford OX1 3LB, UK
| | - Alan P Lewis
- Data and Computational Sciences, GlaxoSmithKline Research and Development, Gunnels Wood Road, Stevenage SG1 2NY, UK
| | - Jiye Shi
- Chemistry Department, UCB Pharma, 216 Bath Road, Slough SL1 3WE, UK
| | - Alexander Bujotzek
- Roche Pharma Research and Early Development, Large Molecule Research, Roche Innovation Center Munich, DE-82377 Penzberg, Germany
| | - Bruck Taddese
- Discovery Sciences Department, AstraZeneca, Granta Park, Cambridge CB21 6GH, UK
| | - Charlotte M Deane
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, 24-29 St Giles’, Oxford OX1 3LB, UK
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Lightwood D, Tservistas M, Zehentleitner M, Sarkar K, Turner A, Bracher M, Smith B, Lamour S, Bourne T, Shaw S, Gozzard N, Palframan RT. Efficacy of an Inhaled IL-13 Antibody Fragment in a Model of Chronic Asthma. Am J Respir Crit Care Med 2019; 198:610-619. [PMID: 29883204 DOI: 10.1164/rccm.201712-2382oc] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
RATIONALE IL-13 is an important cytokine implicated in the pathogenesis of allergic asthma and is an attractive target for an inhaled therapeutic. OBJECTIVE To investigate the efficacy of CDP7766, a nebulized inhaled anti-IL-13 monoclonal antibody Fab fragment, in a model of allergic asthma in cynomolgus macaques naturally sensitized to Ascaris suum. METHODS CDP7766 was nebulized using a vibrating-membrane nebulizer on the basis of eFlow technology. The aerosol generated was analyzed to determine the particle size profile and the biophysical and functional properties of CDP7766. Nebulized CDP7766 (0.1-60 mg/animal, once daily for 5 d) was delivered via the inhaled route. MEASUREMENTS AND MAIN RESULTS The investigational eFlow nebulizer used in this study generated a respirable aerosol of CDP7766 with no evidence of degradation, loss of potency, aggregation, or formation of particulates. Inhaled CDP7766 was well tolerated in the model (no adverse effects related to local irritation) and significantly inhibited BAL allergen-induced cytokine and chemokine upregulation (60 mg vs. vehicle: eotaxin-3, P < 0.0008; MIP [macrophage inflammatory protein]-1β, IL-8, IFN-γ, P ≤ 0.01). CDP7766 significantly inhibited the increase in pulmonary resistance stimulated by inhaled allergen, measured 15 minutes and 24 hours after allergen challenge. CONCLUSION Inhaled CDP7766 potently inhibited the function of IL-13 generated during the airway response to inhaled allergen in cynomolgus macaques, demonstrating the potential of inhaled anti-IL-13 therapeutics for the treatment of allergic asthma.
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Affiliation(s)
| | | | | | | | - Alison Turner
- 1 UCB Pharma, Slough, Berkshire, United Kingdom; and
| | | | - Bryan Smith
- 1 UCB Pharma, Slough, Berkshire, United Kingdom; and
| | | | - Tim Bourne
- 1 UCB Pharma, Slough, Berkshire, United Kingdom; and
| | - Stevan Shaw
- 1 UCB Pharma, Slough, Berkshire, United Kingdom; and
| | - Neil Gozzard
- 1 UCB Pharma, Slough, Berkshire, United Kingdom; and
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Li Q, Barrett A, Vijayakrishnan B, Tiberghien A, Beard R, Rickert KW, Allen KL, Christie RJ, Marelli M, Harper J, Howard P, Wu H, Dall'Acqua WF, Tsui P, Gao C, Borrok MJ. Improved Inhibition of Tumor Growth by Diabody-Drug Conjugates via Half-Life Extension. Bioconjug Chem 2019; 30:1232-1243. [PMID: 30912649 DOI: 10.1021/acs.bioconjchem.9b00170] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Despite some clinical success with antibody-drug conjugates (ADCs) in patients with solid tumors and hematological malignancies, improvements in ADC design are still desirable due to the narrow therapeutic window of these compounds. Tumor-targeting antibody fragments have distinct advantages over monoclonal antibodies, including more rapid tumor accumulation and enhanced penetration, but are subject to rapid clearance. Half-life extension technologies such as PEGylation and albumin-binding domains (ABDs) have been widely used to improve the pharmacokinetics of many different types of biologics. PEGylation improves pharmacokinetics by increasing hydrodynamic size to reduce renal clearance, whereas ABDs extend half-life via FcRn-mediated recycling. In this study, we used an anti-oncofetal antigen 5T4 diabody conjugated with a highly potent cytotoxic pyrrolobenzodiazepine (PBD) warhead to assess and compare the effects of PEGylation and albumin binding on the in vivo efficacy of antibody fragment drug conjugates. Conjugation of 2× PEG20K to a diabody improved half-life from 40 min to 33 h, and an ABD-diabody fusion protein exhibited a half-life of 45 h in mice. In a xenograft model of breast cancer MDA-MB-436, the ABD-diabody-PBD showed greater tumor growth suppression and better tolerability than either PEG-diabody-PBD or diabody-PBD. These results suggest that the mechanism of half-life extension is an important consideration for designing cytotoxic antitumor agents.
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Affiliation(s)
| | | | | | | | - Rhiannon Beard
- Spirogen , 42 New Road , E1 2AX , London , United Kingdom
| | | | | | | | | | | | - Philip Howard
- Spirogen , 42 New Road , E1 2AX , London , United Kingdom
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An Expanded Conformation of an Antibody Fab Region by X-Ray Scattering, Molecular Dynamics, and smFRET Identifies an Aggregation Mechanism. J Mol Biol 2019; 431:1409-1425. [PMID: 30776431 DOI: 10.1016/j.jmb.2019.02.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 02/06/2019] [Accepted: 02/06/2019] [Indexed: 11/20/2022]
Abstract
Protein aggregation is the underlying cause of many diseases, and also limits the usefulness of many natural and engineered proteins in biotechnology. Better mechanistic understanding and characterization of aggregation-prone states is needed to guide protein engineering, formulation, and drug-targeting strategies that prevent aggregation. While several final aggregated states-notably amyloids-have been characterized structurally, very little is known about the native structural conformers that initiate aggregation. We used a novel combination of small-angle x-ray scattering (SAXS), atomistic molecular dynamic simulations, single-molecule Förster resonance energy transfer, and aggregation-prone region predictions, to characterize structural changes in a native humanized Fab A33 antibody fragment, that correlated with the experimental aggregation kinetics. SAXS revealed increases in the native state radius of gyration, Rg, of 2.2% to 4.1%, at pH 5.5 and below, concomitant with accelerated aggregation. In a cutting-edge approach, we fitted the SAXS data to full MD simulations from the same conditions and located the conformational changes in the native state to the constant domain of the light chain (CL). This CL displacement was independently confirmed using single-molecule Förster resonance energy transfer measurements with two dual-labeled Fabs. These conformational changes were also found to increase the solvent exposure of a predicted APR, suggesting a likely mechanism through which they promote aggregation. Our findings provide a means by which aggregation-prone conformational states can be readily determined experimentally, and thus potentially used to guide protein engineering, or ligand binding strategies, with the aim of stabilizing the protein against aggregation.
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Ma H, Ó'Fágáin C, O'Kennedy R. Unravelling enhancement of antibody fragment stability – Role of format structure and cysteine modification. J Immunol Methods 2019; 464:57-63. [DOI: 10.1016/j.jim.2018.10.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 09/11/2018] [Accepted: 10/22/2018] [Indexed: 01/08/2023]
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13
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Khoee S, Yousefalizadeh G, Kavand A. Preparation of dual-targeted redox-responsive nanogels based on pegylated sorbitan for targeted and antitumor drug delivery. Eur Polym J 2017. [DOI: 10.1016/j.eurpolymj.2017.08.030] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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14
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In silico methods for design of biological therapeutics. Methods 2017; 131:33-65. [PMID: 28958951 DOI: 10.1016/j.ymeth.2017.09.008] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 09/21/2017] [Accepted: 09/23/2017] [Indexed: 12/18/2022] Open
Abstract
It has been twenty years since the first rationally designed small molecule drug was introduced into the market. Since then, we have progressed from designing small molecules to designing biotherapeutics. This class of therapeutics includes designed proteins, peptides and nucleic acids that could more effectively combat drug resistance and even act in cases where the disease is caused because of a molecular deficiency. Computational methods are crucial in this design exercise and this review discusses the various elements of designing biotherapeutic proteins and peptides. Many of the techniques discussed here, such as the deterministic and stochastic design methods, are generally used in protein design. We have devoted special attention to the design of antibodies and vaccines. In addition to the methods for designing these molecules, we have included a comprehensive list of all biotherapeutics approved for clinical use. Also included is an overview of methods that predict the binding affinity, cell penetration ability, half-life, solubility, immunogenicity and toxicity of the designed therapeutics. Biotherapeutics are only going to grow in clinical importance and are set to herald a new generation of disease management and cure.
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Affiliation(s)
- Madduri Srinivasarao
- Purdue Institute for Drug
Discovery, Purdue University, West Lafayette, Indiana 47907, United States
| | - Philip S. Low
- Purdue Institute for Drug
Discovery, Purdue University, West Lafayette, Indiana 47907, United States
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16
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Discovery and Characterization of a Novel CD4-Binding Adnectin with Potent Anti-HIV Activity. Antimicrob Agents Chemother 2017; 61:AAC.00508-17. [PMID: 28584151 DOI: 10.1128/aac.00508-17] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 05/30/2017] [Indexed: 02/08/2023] Open
Abstract
A novel fibronectin-based protein (Adnectin) HIV-1 inhibitor was generated using in vitro selection. This inhibitor binds to human CD4 with a high affinity (3.9 nM) and inhibits viral entry at a step after CD4 engagement and preceding membrane fusion. The progenitor sequence of this novel inhibitor was selected from a library of trillions of Adnectin variants using mRNA display and then further optimized for improved antiviral and physical properties. The final optimized inhibitor exhibited full potency against a panel of 124 envelope (gp160) proteins spanning 11 subtypes, indicating broad-spectrum activity. Resistance profiling studies showed that this inhibitor required 30 passages (151 days) in culture to acquire sufficient resistance to result in viral titer breakthrough. Resistance mapped to the loss of multiple potential N-linked glycosylation sites in gp120, suggesting that inhibition is due to steric hindrance of CD4-binding-induced conformational changes.
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Hu QY, Berti F, Adamo R. Towards the next generation of biomedicines by site-selective conjugation. Chem Soc Rev 2016; 45:1691-719. [PMID: 26796469 DOI: 10.1039/c4cs00388h] [Citation(s) in RCA: 116] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Bioconjugates represent an emerging class of medicines, which offer therapeutic opportunities overtaking those of the individual components. Many novel bioconjugates have been explored in order to address various emerging medical needs. The last decade has witnessed the exponential growth of new site-selective bioconjugation techniques, however very few methods have made the way into human clinical trials. Here we discuss various applications of site-selective conjugation in biomedicines, including half-life extension, antibody-drug conjugates, conjugate vaccines, bispecific antibodies and cell therapy. The review is intended to highlight both the progress and challenges, and identify a potential roadmap to address the gap.
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Affiliation(s)
- Qi-Ying Hu
- Novartis Institutes for Biomedical Research (NIBR), 100 Technology Square, Cambridge, MA 02139, USA.
| | - Francesco Berti
- GSK Vaccines (former Novartis Vaccines & Diagnostics), Via Fiorentina 1, 53100 Siena, Italy.
| | - Roberto Adamo
- GSK Vaccines (former Novartis Vaccines & Diagnostics), Via Fiorentina 1, 53100 Siena, Italy.
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18
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Hong JY, Bae JH, Lee KE, Kim M, Kim MH, Kang HJ, Park EH, Yoo KS, Jeong SK, Kim KW, Kim KE, Sohn MH. Antibody to FcεRIα Suppresses Immunoglobulin E Binding to High-Affinity Receptor I in Allergic Inflammation. Yonsei Med J 2016; 57:1412-9. [PMID: 27593869 PMCID: PMC5011273 DOI: 10.3349/ymj.2016.57.6.1412] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 03/21/2016] [Accepted: 03/24/2016] [Indexed: 11/27/2022] Open
Abstract
PURPOSE High-affinity receptor I (FcεRI) on mast cells and basophils plays a key role in the immunoglobulin E (IgE)-mediated type I hypersensitivity mediated by allergen cross-linking of the specific IgE-FcεRI complex. Thus, prevention of IgE binding to FcεRI on these cells is an effective therapy for allergic disease. We have developed a strategy to disrupt IgE binding to FcεRI using an antibody targeting FcεRIα. MATERIALS AND METHODS Fab fragment antibodies, which lack the Fc domain, with high affinity and specificity for FcεRIα and effective inhibitory activity against IgE-FcεRI binding were screened. IgE-induced histamine, β-hexosaminidase and Ca²⁺ release in basophils were determined by ELISA. A B6.Cg-Fcer1a(tm1Knt) Tg(FCER1A)1Bhk/J mouse model of passive cutaneous anaphylaxis (PCA) was used to examine the inhibitory effect of NPB311 on allergic skin inflammation. RESULTS NPB311 exhibited high affinity to human FcεRIα (KD=4 nM) and inhibited histamine, β-hexosaminidase and Ca²⁺ release in a concentration-dependent manner in hFcεRI-expressing cells. In hFcεRIα-expressing mice, dye leakage was higher in the PCA group than in controls, but decreased after NPB311 treatment. NPB311 could form a complex with FcεRIα and inhibit the release of inflammation mediators. CONCLUSION Our approach for producing anti-FcεRIα Fab fragment antibody NPB311 may enable clinical application to a therapeutic pathway in IgE/FcεRI-mediated diseases.
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Affiliation(s)
- Jung Yeon Hong
- Department of Pediatrics and Institute of Allergy, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | | | - Kyung Eun Lee
- Department of Pediatrics and Institute of Allergy, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - Mina Kim
- Department of Pediatrics and Institute of Allergy, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - Min Hee Kim
- CRID Center, NeoPharm Co., Ltd., Daejeon, Korea
| | | | | | | | | | - Kyung Won Kim
- Department of Pediatrics and Institute of Allergy, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - Kyu Earn Kim
- Department of Pediatrics and Institute of Allergy, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - Myung Hyun Sohn
- Department of Pediatrics and Institute of Allergy, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea.
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19
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Clinical Pharmacokinetics and Pharmacodynamics of Monoclonal Antibodies Approved to Treat Rheumatoid Arthritis. Clin Pharmacokinet 2016; 54:1107-23. [PMID: 26123705 DOI: 10.1007/s40262-015-0296-9] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Monoclonal antibodies (mAbs) are increasingly used to treat rheumatoid arthritis (RA). At present, anti-tumor necrosis factor-α drugs (infliximab, adalimumab, certolizumab pegol, and golimumab), rituximab, and tocilizumab are approved for RA treatment. This review focuses on the pharmacokinetics and pharmacodynamics of mAbs approved in RA. Being large proteins, mAbs exhibit complex pharmacokinetic and pharmacodynamic properties. In particular, owing to the interactions of mAbs with their antigenic targets, the pharmacokinetics of mAbs depends on target turnover and exhibits non-specific (linear) and target-mediated (often nonlinear) clearances. Their volume of distribution is low (3-4 L) and their elimination half-life usually ranges from 2 to 3 weeks. The inter-individual pharmacokinetic variability of mAbs is usually large and is partly explained by differences in antigenic burden or by anti-drug antibodies, which accelerate mAb elimination. The inter-individual variability of clinical response is large and influenced by the pharmacokinetics. The analysis of mAbs concentration-effect relationship relies more and more often on pharmacokinetic-pharmacodynamic modeling; these models being suitable for dosing optimization. Even if adverse effects of mAbs used in RA are well known, the relationship between mAb concentration and adverse effects is poorly documented, especially for anti-tumor necrosis factor-α mAbs. Overall, RA patients treated with mAbs should benefit from individualized dosing strategies. Because of the complexity of their pharmacokinetics and mechanisms of action, the current dosing strategy of mAbs is not based on sound knowledge. New studies are needed to assess individual dosing regimen, adjusted notably to disease activity.
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20
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Monovalent Fc receptor blockade by an anti–Fcγ receptor/albumin fusion protein ameliorates murine ITP with abrogated toxicity. Blood 2016; 127:132-8. [DOI: 10.1182/blood-2015-08-664656] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 10/18/2015] [Indexed: 11/20/2022] Open
Abstract
Key Points
We generated a novel monovalent anti-FcγRIII/albumin fusion protein that ameliorates antibody-mediated murine ITP. Severe adverse events by anti-FcγR antibodies because of FcγR cross-linking are overcome by monovalent FcγR blockade.
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21
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Gong J, Gu X, Achanzar WE, Chadwick KD, Gan J, Brock BJ, Kishnani NS, Humphreys WG, Iyer RA. Quantitative analysis of polyethylene glycol (PEG) and PEGylated proteins in animal tissues by LC-MS/MS coupled with in-source CID. Anal Chem 2014; 86:7642-9. [PMID: 25003239 DOI: 10.1021/ac501507g] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The covalent conjugation of polyethylene glycol (PEG, typical MW > 10k) to therapeutic peptides and proteins is a well-established approach to improve their pharmacokinetic properties and diminish the potential for immunogenicity. Even though PEG is generally considered biologically inert and safe in animals and humans, the slow clearance of large PEGs raises concerns about potential adverse effects resulting from PEG accumulation in tissues following chronic administration, particularly in the central nervous system. The key information relevant to the issue is the disposition and fate of the PEG moiety after repeated dosing with PEGylated proteins. Here, we report a novel quantitative method utilizing LC-MS/MS coupled with in-source CID that is highly selective and sensitive to PEG-related materials. Both (40K)PEG and a tool PEGylated protein (ATI-1072) underwent dissociation in the ionization source of mass spectrometer to generate a series of PEG-specific ions, which were subjected to further dissociation through conventional CID. To demonstrate the potential application of the method to assess PEG biodistribution following PEGylated protein administration, a single dose study of ATI-1072 was conducted in rats. Plasma and various tissues were collected, and the concentrations of both (40K)PEG and ATI-1072 were determined using the LC-MS/MS method. The presence of (40k)PEG in plasma and tissue homogenates suggests the degradation of PEGylated proteins after dose administration to rats, given that free PEG was absent in the dosing solution. The method enables further studies for a thorough characterization of disposition and fate of PEGylated proteins.
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Affiliation(s)
- Jiachang Gong
- Pharmaceutical Candidate Optimization, Bristol-Myers Squibb Company , Lawrenceville, New Jersey 08540, United States
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22
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Ding S, Song M, Sim BC, Gu C, Podust VN, Wang CW, McLaughlin B, Shah TP, Lax R, Gast R, Sharan R, Vasek A, Hartman MA, Deniston C, Srinivas P, Schellenberger V. Multivalent antiviral XTEN-peptide conjugates with long in vivo half-life and enhanced solubility. Bioconjug Chem 2014; 25:1351-9. [PMID: 24932887 PMCID: PMC4157762 DOI: 10.1021/bc500215m] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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XTENs are unstructured, nonrepetitive
protein polymers designed
to prolong the in vivo half-life of pharmaceuticals by introducing
a bulking effect similar to that of poly(ethylene glycol). While XTEN
can be expressed as a recombinant fusion protein with bioactive proteins
and peptides, therapeutic molecules of interest can also be chemically
conjugated to XTEN. Such an approach permits precise control over
the positioning, spacing, and valency of bioactive moieties along
the length of XTEN. We have demonstrated the attachment of T-20, an
anti-retroviral peptide indicated for the treatment of HIV-1 patients
with multidrug resistance, to XTEN. By reacting maleimide-functionalized
T-20 with cysteine-containing XTENs and varying the number and positioning
of cysteines in the XTENs, a library of different peptide–polymer
combinations were produced. The T-20-XTEN conjugates were tested using
an in vitro antiviral assay and were found to be effective in inhibiting
HIV-1 entry and preventing cell death, with the copy number and spacing
of the T-20 peptides influencing antiviral activity. The peptide–XTEN
conjugates were also discovered to have enhanced solubilities in comparison
with the native T-20 peptide. The pharmacokinetic profile of the most
active T-20-XTEN conjugate was measured in rats, and it was found
to exhibit an elimination half-life of 55.7 ± 17.7 h, almost
20 times longer than the reported half-life for T-20 dosed in rats.
As the conjugation of T-20 to XTEN greatly improved the in vivo half-life
and solubility of the peptide, the XTEN platform has been demonstrated
to be a versatile tool for improving the properties of drugs and enabling
the development of a class of next-generation therapeutics.
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Affiliation(s)
- Sheng Ding
- Amunix Operating Inc. , 500 Ellis Street, Mountain View, California 94043 United States
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23
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Abstract
Monoclonal antibodies have been successfully used for the therapy of various diseases. However, because of their large size (∼150 kD), many limitations have also been found during their development and manufacture. The use of antibody fragments with smaller sizes is one of the strategies to overcome these limitations. Antibody heavy chain variable domains (12∼15 kD) have already been widely used for the development of variable domain-based engineered antibody domains (termed V-based eAds) targeting different antigens. Recently, antibody second heavy chain constant domains (∼12 kD) were proposed as novel scaffolds for library construction and selection of specific binders termed constant domain-based eAds (C-based eAds) as novel candidate therapeutics, which might also confer additional crystallizable fragment functions. Both V- and C-based eAds are promising therapeutic candidates. This review summarizes progress in the development of eAds, and discusses the related patents and their potential applications.
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24
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Ding H, Carlton MM, Povoski SP, Milum K, Kumar K, Kothandaraman S, Hinkle GH, Colcher D, Brody R, Davis PD, Pokora A, Phelps M, Martin EW, Tweedle MF. Site specific discrete PEGylation of (124)I-labeled mCC49 Fab' fragments improves tumor MicroPET/CT imaging in mice. Bioconjug Chem 2013; 24:1945-54. [PMID: 24175669 DOI: 10.1021/bc400375f] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The tumor-associated glycoprotein-72 (TAG-72) antigen is highly overexpressed in various human adenocarcinomas and anti-TAG-72 monoclonal antibodies, and fragments are therefore useful as pharmaceutical targeting vectors. In this study, we investigated the effects of site-specific PEGylation with MW 2-4 kDa discrete, branched PEGylation reagents on mCC49 Fab' (MW 50 kDa) via in vitro TAG72 binding, and in vivo blood clearance kinetics, biodistribution, and mouse tumor microPET/CT imaging. mCC49Fab' (Fab'-NEM) was conjugated at a hinge region cysteine with maleimide-dPEG 12-(dPEG24COOH)3 acid (Mal-dPEG-A), maleimide-dPEG12-(dPEG12COOH)3 acid (Mal-dPEG-B), or maleimide-dPEG12-(m-dPEG24)3 (Mal-dPEG-C), and then radiolabeled with iodine-124 ((124)I) in vitro radioligand binding assays and in vivo studies used TAG-72 expressing LS174T human colon carcinoma cells and xenograft mouse tumors. Conjugation of mCC49Fab' with Mal-dPEG-A (Fab'-A) reduced the binding affinity of the non PEGylated Fab' by 30%; however, in vivo, Fab'-A significantly lengthened the blood retention vs Fab'-NEM (47.5 vs 28.1%/ID at 1 h, 25.1 vs 8.4%/ID at 5 h, p < 0.01), showed excellent tumor to background, better microPET/CT images due to higher tumor accumulation, and increased tumor concentration in excised tissues at 72 h by 130% (5.09 ± 0.83 vs 3.83 ± 1.50%ID/g, p < 0.05). Despite the strong similarity of the three PEGylation reagents, PEGylation with Mal-dPEG-B or -C reduced the in vitro binding affinity of Fab'-NEM by 70%, blood retention, microPET/CT imaging tumor signal intensity, and residual 72 h tumor concentration by 49% (3.83 ± 1.50 vs 1.97 ± 0.29%ID/g, p < 0.05) and 63% (3.83 ± 1.50 vs 1.42 ± 0.35%ID/g, p < 0.05), respectively. We conclude that remarkably subtle changes in the structure of the PEGylation reagent can create significantly altered biologic behavior. Further study is warranted of conjugates of the triple branched, negatively charged Mal-dPEG-A.
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Affiliation(s)
- Haiming Ding
- Department of Radiology, The Wright Center for Innovation in Biomedical Imaging, ‡Department of Surgery, and ⊥Department of Pharmacology, The Ohio State University , Columbus, Ohio 43210, United States
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