1
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Diemer V, Roy E, Agouridas V, Melnyk O. Protein desulfurization and deselenization. Chem Soc Rev 2024. [PMID: 39010733 DOI: 10.1039/d4cs00135d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
Abstract
Methods enabling the dechalcogenation of thiols or selenols have been investigated and developed for a long time in fields of research as diverse as the study of prebiotic chemistry, the engineering of fuel processing techniques, the study of biomolecule structures and function or the chemical synthesis of biomolecules. The dechalcogenation of thiol or selenol amino acids is nowadays a particularly flourishing area of research for being a pillar of modern chemical protein synthesis, when used in combination with thiol or selenol-based chemoselective peptide ligation chemistries. This review offers a comprehensive and scholarly overview of the field, emphasizing emerging trends and providing a detailed and critical mechanistic discussion of the dechalcogenation methods developed so far. Taking advantage of recently published reports, it also clarifies some unexpected desulfurization reactions that were observed in the past and for which no explanation was provided at the time. Additionally, the review includes a discussion on principal desulfurization methods within the framework of newly introduced green chemistry metrics and toolkits, providing a well-rounded exploration of the subject.
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Affiliation(s)
- Vincent Diemer
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017, Center for Infection and Immunity of Lille, F-59000 Lille, France.
| | - Eliott Roy
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017, Center for Infection and Immunity of Lille, F-59000 Lille, France.
| | - Vangelis Agouridas
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017, Center for Infection and Immunity of Lille, F-59000 Lille, France.
- Centrale Lille, F-59000 Lille, France
| | - Oleg Melnyk
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017, Center for Infection and Immunity of Lille, F-59000 Lille, France.
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2
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Kretschmer K, Stichel J, Bellmann-Sickert K, Baumann L, Bierer D, Riedl B, Beck-Sickinger AG. Pinpointing the interaction site between semaphorin-3A and its inhibitory peptide. J Pept Sci 2023; 29:e3460. [PMID: 36285908 DOI: 10.1002/psc.3460] [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: 07/25/2022] [Revised: 10/18/2022] [Accepted: 10/19/2022] [Indexed: 11/05/2022]
Abstract
Semaphorin-3A (Sema-3A) is a chemorepellant protein with various biological functions, including kidney development. It interacts with a protein complex consisting of the receptors neuropilin-1 (NRP-1) and plexin-A1. After acute kidney injury, Sema-3A is overexpressed and secreted, leading to a loss of kidney function. The development of peptide inhibitors is a promising approach to modulate the interaction of Sema-3A with its receptor NRP-1. Few interaction points between these binding partners are known. However, an immunoglobulin-like domain-derived peptide of Sema-3A has shown a positive effect on cell proliferation. To specify these interactions between the peptide inhibitor and the Sema-3A-NRP-1 system, the peptides were modified with the photoactivatable amino acids 4-benzoyl-l-phenylalanine or photo-l-leucine by solid-phase peptide synthesis. Activity was tested by an enzyme-linked immunosorbent-based binding assay, and crosslinking experiments were analyzed by Western blot and mass spectrometry, demonstrating a specific binding site of the peptide at Sema-3A. The observed signals for Sema-3A-peptide interaction were found in a defined area of the Sema domain, which was also demonstrated to be involved in NRP-1 binding. The presented data identified the interaction site for further development of therapeutic peptides to treat acute kidney injury by blocking the Sema-3A-NRP-1 interaction.
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Affiliation(s)
- Kevin Kretschmer
- Institute of Biochemistry, Faculty of Life Sciences, Leipzig University, Leipzig, Germany
| | - Jan Stichel
- Institute of Biochemistry, Faculty of Life Sciences, Leipzig University, Leipzig, Germany
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3
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A Review on Forced Degradation Strategies to Establish the Stability of Therapeutic Peptide Formulations. Int J Pept Res Ther 2023. [DOI: 10.1007/s10989-023-10492-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
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4
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In vitro and in vivo immunogenicity assessment of protein aggregate characteristics. Int J Pharm 2023; 631:122490. [PMID: 36521637 DOI: 10.1016/j.ijpharm.2022.122490] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 12/06/2022] [Accepted: 12/08/2022] [Indexed: 12/14/2022]
Abstract
The immunogenicity risk of therapeutic protein aggregates has been extensively investigated over the past decades. While it is established that not all aggregates are equally immunogenic, the specific aggregate characteristics, which are most likely to induce an immune response, remain ambiguous. The aim of this study was to perform comprehensive in vitro and in vivo immunogenicity assessment of human insulin aggregates varying in size, structure and chemical modifications, while keeping other morphological characteristics constant. We found that flexible aggregates with highly altered secondary structure were most immunogenic in all setups, while compact aggregates with native-like structure were found to be immunogenic primarily in vivo. Moreover, sub-visible (1-100 µm) aggregates were found to be more immunogenic than sub-micron (0.1-1 µm) aggregates, while chemical modifications (deamidation, ethylation and covalent dimers) were not found to have any measurable impact on immunogenicity. The findings highlight the importance of utilizing aggregates varying in few characteristics for assessment of immunogenicity risk of specific morphological features and may provide a workflow for reliable particle analysis in biotherapeutics.
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5
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Gary S, Bloom S. Peptide Carbocycles: From -SS- to -CC- via a Late-Stage "Snip-and-Stitch". ACS CENTRAL SCIENCE 2022; 8:1537-1547. [PMID: 36439308 PMCID: PMC9686213 DOI: 10.1021/acscentsci.2c00456] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Indexed: 05/28/2023]
Abstract
One way to improve the therapeutic potential of peptides is through cyclization. This is commonly done using a disulfide bond between two cysteine residues in the peptide. However, disulfide bonds are susceptible to reductive cleavage, and this can deactivate the peptide and endanger endogenous proteins through covalent modification. Substituting disulfide bonds with more chemically robust carbon-based linkers has proven to be an effective strategy to better develop cyclic peptides as drugs, but finding the optimal carbon replacement is synthetically laborious. We report a new late-stage platform wherein a single disulfide bond in a cyclic peptide can serve as the progenitor for any number of new carbon-rich groups, derived from organodiiodides, using a Zn:Cu couple and a hydrosilane. We show that this platform can furnish entirely new carbocyclic scaffolds with enhanced permeability and structural integrity and that the stereochemistry of the new cycles can be biased by a judicious choice in silane.
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Affiliation(s)
- Samuel Gary
- Department of Medicinal Chemistry, University of Kansas, Lawrence, Kansas66045, United States
| | - Steven Bloom
- Department of Medicinal Chemistry, University of Kansas, Lawrence, Kansas66045, United States
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6
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Assembly of Biologically Functional Structures by Nucleic Acid Templating: Implementation of a Strategy to Overcome Inhibition by Template Excess. Molecules 2022; 27:molecules27206831. [PMID: 36296424 PMCID: PMC9610079 DOI: 10.3390/molecules27206831] [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: 08/26/2022] [Revised: 10/06/2022] [Accepted: 10/07/2022] [Indexed: 11/18/2022] Open
Abstract
Delivery of therapeutic molecules to pathogenic cells is often hampered by unintended toxicity to normal cells. In principle, this problem can be circumvented if the therapeutic effector molecule is split into two inactive components, and only assembled on or within the target cell itself. Such an in situ process can be realized by exploiting target-specific molecules as templates to direct proximity-enhanced assembly. Modified nucleic acids carrying inert precursor fragments can be designed to co-hybridize on a target-specific template nucleic acid, such that the enforced proximity accelerates assembly of a functional molecule for antibody recognition. We demonstrate the in vitro feasibility of this adaptation of nucleic acid-templated synthesis (NATS) using oligonucleotides bearing modified peptides (“haplomers”), for templated assembly of a mimotope recognized by the therapeutic antibody trastuzumab. Enforced proximity promotes mimotope assembly via traceless native chemical ligation. Nevertheless, titration of participating haplomers through template excess is a potential limitation of trimolecular NATS. In order to overcome this problem, we devised a strategy where haplomer hybridization can only occur in the presence of target, without being subject to titration effects. This generalizable NATS modification may find future applications in enabling directed targeting of pathological cells.
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7
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Scott TA, Verest M, Farnung J, Forneris CC, Robinson SL, Ji X, Hubrich F, Chepkirui C, Richter DU, Huber S, Rust P, Streiff AB, Zhang Q, Bode JW, Piel J. Widespread microbial utilization of ribosomal β-amino acid-containing peptides and proteins. Chem 2022. [DOI: 10.1016/j.chempr.2022.09.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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8
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Clark ET, Sievers EE, Debelouchina GT. A Chemical Biology Primer for NMR Spectroscopists. JOURNAL OF MAGNETIC RESONANCE OPEN 2022; 10-11:100044. [PMID: 35494416 PMCID: PMC9053072 DOI: 10.1016/j.jmro.2022.100044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Among structural biology techniques, NMR spectroscopy offers unique capabilities that enable the atomic resolution studies of dynamic and heterogeneous biological systems under physiological and native conditions. Complex biological systems, however, often challenge NMR spectroscopists with their low sensitivity, crowded spectra or large linewidths that reflect their intricate interaction patterns and dynamics. While some of these challenges can be overcome with the development of new spectroscopic approaches, chemical biology can also offer elegant and efficient solutions at the sample preparation stage. In this tutorial, we aim to present several chemical biology tools that enable the preparation of selectively and segmentally labeled protein samples, as well as the introduction of site-specific spectroscopic probes and post-translational modifications. The four tools covered here, namely cysteine chemistry, inteins, native chemical ligation, and unnatural amino acid incorporation, have been developed and optimized in recent years to be more efficient and applicable to a wider range of proteins than ever before. We briefly introduce each tool, describe its advantages and disadvantages in the context of NMR experiments, and offer practical advice for sample preparation and analysis. We hope that this tutorial will introduce beginning researchers in the field to the possibilities chemical biology can offer to NMR spectroscopists, and that it will inspire new and exciting applications in the quest to understand protein function in health and disease.
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Affiliation(s)
- Evan T. Clark
- Department of Chemistry and Biochemistry, Division of Physical Sciences, University of California, San Diego, La Jolla, CA 92093, U.S.A
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, U.S.A
| | - Elanor E. Sievers
- Department of Chemistry and Biochemistry, Division of Physical Sciences, University of California, San Diego, La Jolla, CA 92093, U.S.A
| | - Galia T. Debelouchina
- Department of Chemistry and Biochemistry, Division of Physical Sciences, University of California, San Diego, La Jolla, CA 92093, U.S.A
- Corresponding author: Galia Debelouchina, University of California, San Diego, Natural Sciences Building 4322, 9500 Gilman Dr., La Jolla, CA 92093, 858-534-3038,
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9
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Rossetto D, Valer L, Yeh Martín N, Guella G, Hongo Y, Mansy SS. Prebiotic Environments with Mg 2+ and Thiophilic Metal Ions Increase the Thermal Stability of Cysteine and Non-cysteine Peptides. ACS EARTH & SPACE CHEMISTRY 2022; 6:1221-1226. [PMID: 35620317 PMCID: PMC9126146 DOI: 10.1021/acsearthspacechem.2c00042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 04/13/2022] [Accepted: 04/14/2022] [Indexed: 06/15/2023]
Abstract
Wet-dry cycles driven by heating to high temperatures are frequently invoked for the prebiotic synthesis of peptides. Similarly, iron-sulfur clusters are often cited as an example of an ancient catalyst that helped prune early chemical systems into metabolic-like pathways. Because extant iron-sulfur clusters are metallocofactors of protein enzymes and nearly ubiquitous across biology, a reasonable hypothesis is that prebiotic iron-sulfur peptides formed on the early Earth. However, iron-sulfur clusters are coordinated by multiple cysteine residues, and the stability of cysteines to the heat steps of wet-dry cycles has not been determined. It, therefore, has remained unclear if the peptides needed to stabilize the formation of iron-sulfur clusters could have formed. If not, then iron-sulfur-dependent activity may have emerged later, when milder, more biological-like peptide synthesis machinery took hold. Here, we report the thermal stability of cysteine-containing peptides. We show that temperatures of 150 °C lead to the rapid degradation of cysteinyl peptides. However, the presence of Mg2+ at environmentally reasonable concentrations leads to significant protection. Thiophilic metal ions also protect against degradation at 150 °C but require concentrations not frequently observed in the environment. Nevertheless, cysteine-containing peptides are stable at lower, prebiotically plausible temperatures in seawater, carbonate lake, and ferrous lake conditions. The data are consistent with the persistence of cysteine-containing peptides on the early Earth in environments rich in metal ions. High concentrations of Mg2+ are common intra- and extra-cellularly, suggesting that the protection afforded by Mg2+ may reflect conditions that were present on the prebiotic Earth.
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Affiliation(s)
- Daniele Rossetto
- D-CIBIO, University of Trento, Via Sommarive 9, 38123 Povo, Italy
- Department
of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, Alberta T6G 2G2, Canada
| | - Luca Valer
- D-CIBIO, University of Trento, Via Sommarive 9, 38123 Povo, Italy
- Department
of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, Alberta T6G 2G2, Canada
| | - Noël Yeh Martín
- D-CIBIO, University of Trento, Via Sommarive 9, 38123 Povo, Italy
| | - Graziano Guella
- Department
of Physics, University of Trento, Via Sommarive 14, 38123 Povo, Italy
| | - Yayoi Hongo
- Earth-Life
Science Institute, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan
- Okinawa
Institute of Science and Technology Graduate University, Onna-son, Kunigami, Okinawa 904-0495, Japan
| | - Sheref S. Mansy
- D-CIBIO, University of Trento, Via Sommarive 9, 38123 Povo, Italy
- Department
of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, Alberta T6G 2G2, Canada
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10
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Procopio-Melino R, Kotch FW, Prashad AS, Gomes JM, Wang W, Arve B, Dawdy A, Chen L, Sperry J, Hosselet C, He T, Kriz R, Lin L, Marquette K, Tchistiakova L, Somers W, Rouse JC, Zhong X. Cysteine metabolic engineering and selective disulfide reduction produce superior antibody-drug-conjugates. Sci Rep 2022; 12:7262. [PMID: 35508689 PMCID: PMC9068625 DOI: 10.1038/s41598-022-11344-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 04/18/2022] [Indexed: 11/30/2022] Open
Abstract
Next-generation site-specific cysteine-based antibody–drug-conjugates (ADCs) broaden therapeutic index by precise drug-antibody attachments. However, manufacturing such ADCs for clinical validation requires complex full reduction and reoxidation processes, impacting product quality. To overcome this technical challenge, we developed a novel antibody manufacturing process through cysteine (Cys) metabolic engineering in Chinese hamster ovary cells implementing a unique cysteine-capping technology. This development enabled a direct conjugation of drugs after chemoselective-reduction with mild reductant tris(3-sulfonatophenyl)phosphine. This innovative platform produces clinical ADC products with superior quality through a simplified manufacturing process. This technology also has the potential to integrate Cys-based site-specific conjugation with other site-specific conjugation methodologies to develop multi-drug ADCs and exploit multi-mechanisms of action for effective cancer treatments.
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Affiliation(s)
- Renée Procopio-Melino
- BioProcess R&D, Biotherapeutics Pharmaceutical Sciences, Medicinal Sciences, Pfizer Worldwide R&D, 1 Burtt Road, Andover, MA, 01810, USA
| | - Frank W Kotch
- BioProcess R&D, Biotherapeutics Pharmaceutical Sciences, Medicinal Sciences, Pfizer Worldwide R&D, 875 Chesterfield Parkway West, Chesterfield, MO, 63017, USA.
| | - Amar S Prashad
- BioProcess R&D, Biotherapeutics Pharmaceutical Sciences, Medicinal Sciences, Pfizer Worldwide R&D, 875 Chesterfield Parkway West, Chesterfield, MO, 63017, USA.,Pearl River Laboratories Inc, 401 North Middletown Road, Pearl River, NY, 10965, USA
| | - Jose M Gomes
- BioProcess R&D, Biotherapeutics Pharmaceutical Sciences, Medicinal Sciences, Pfizer Worldwide R&D, 1 Burtt Road, Andover, MA, 01810, USA.
| | - Wenge Wang
- BioProcess R&D, Biotherapeutics Pharmaceutical Sciences, Medicinal Sciences, Pfizer Worldwide R&D, 1 Burtt Road, Andover, MA, 01810, USA
| | - Bo Arve
- BioProcess R&D, Biotherapeutics Pharmaceutical Sciences, Medicinal Sciences, Pfizer Worldwide R&D, 875 Chesterfield Parkway West, Chesterfield, MO, 63017, USA
| | - Andrew Dawdy
- Analytical R&D, Biotherapeutics Pharmaceutical Sciences, Medicinal Sciences, Pfizer Worldwide R&D, 875 Chesterfield Parkway West, Chesterfield, MO, 63017, USA.
| | - Lawrence Chen
- Analytical R&D, Biotherapeutics Pharmaceutical Sciences, Medicinal Sciences, Pfizer Worldwide R&D, 1 Burtt Road, Andover, MA, 01810, USA
| | - Justin Sperry
- Analytical R&D, Biotherapeutics Pharmaceutical Sciences, Medicinal Sciences, Pfizer Worldwide R&D, 875 Chesterfield Parkway West, Chesterfield, MO, 63017, USA
| | - Christine Hosselet
- Vaccine Research, Pfizer Worldwide R&D, 401 North Middletown Road, Pearl River, NY, 10965, USA
| | - Tao He
- BioMedicine Design, Medicinal Sciences, Pfizer Worldwide R&D, 610 Main Street, Cambridge, MA, 02139, USA.,JOINN Biologics US Inc., 2600 Hilltop Dr., Richmond, CA, 94806, USA
| | - Ronald Kriz
- BioMedicine Design, Medicinal Sciences, Pfizer Worldwide R&D, 610 Main Street, Cambridge, MA, 02139, USA
| | - Laura Lin
- BioMedicine Design, Medicinal Sciences, Pfizer Worldwide R&D, 610 Main Street, Cambridge, MA, 02139, USA
| | - Kimberly Marquette
- BioMedicine Design, Medicinal Sciences, Pfizer Worldwide R&D, 610 Main Street, Cambridge, MA, 02139, USA
| | - Lioudmila Tchistiakova
- BioMedicine Design, Medicinal Sciences, Pfizer Worldwide R&D, 610 Main Street, Cambridge, MA, 02139, USA
| | - Will Somers
- BioMedicine Design, Medicinal Sciences, Pfizer Worldwide R&D, 610 Main Street, Cambridge, MA, 02139, USA
| | - Jason C Rouse
- Analytical R&D, Biotherapeutics Pharmaceutical Sciences, Medicinal Sciences, Pfizer Worldwide R&D, 1 Burtt Road, Andover, MA, 01810, USA
| | - Xiaotian Zhong
- BioMedicine Design, Medicinal Sciences, Pfizer Worldwide R&D, 610 Main Street, Cambridge, MA, 02139, USA.
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11
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Zhang Z, Chow SY, De Guzman R, Joh NH, Joubert MK, Richardson J, Shah B, Wikström M, Zhou ZS, Wypych J. A Mass Spectrometric Characterization of Light-Induced Modifications in Therapeutic Proteins. J Pharm Sci 2022; 111:1556-1564. [DOI: 10.1016/j.xphs.2022.02.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 02/04/2022] [Accepted: 02/04/2022] [Indexed: 12/15/2022]
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12
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Degterev M, Smolov M, Shukurov R. Improvement of the Degradation Profiling of Eculizumab and Omalizumab Monoclonal Antibodies by Liquid Chromatography–Mass Spectrometry. JOURNAL OF ANALYTICAL CHEMISTRY 2021. [DOI: 10.1134/s1061934821140033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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13
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Lamarche J, Alcoceba Álvarez E, Cordeau E, Enjalbal C, Massai L, Messori L, Lobinski R, Ronga L. Comparative reactivity of medicinal gold(I) compounds with the cyclic peptide vasopressin and its diselenide analogue. Dalton Trans 2021; 50:17487-17490. [PMID: 34796892 DOI: 10.1039/d1dt03470g] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The reactions of the medicinal gold(I) compound auranofin and its close analogues with vasopressin and the diselenide analogue were comparatively investigated by LC-electrospray MS/MS. Evidence is gained of the possible cleavage of the S-S and Se-Se bridges induced by Au(I). Notably, we found that, in the absence of reducing agents, the sulfur and selenium atoms are metallated only at high temperature (70 °C) with the preferential binding of gold to selenium. The reaction with the S-S bridge can take place at physiological temperature (37 °C) under reducing conditions. The implications of these results are discussed in the general frame of the reactivity of biologically relevant soft Lewis acids with peptides and proteins.
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Affiliation(s)
- Jeremy Lamarche
- Université de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France.
| | | | | | | | - Lara Massai
- Department of Chemistry, University of Florence, Via della Lastruccia 3-13, 50019 Sesto Fiorentino, Italy
| | - Luigi Messori
- Department of Chemistry, University of Florence, Via della Lastruccia 3-13, 50019 Sesto Fiorentino, Italy
| | - Ryszard Lobinski
- Université de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France. .,IM Sechenov First Moscow State Medical University (Sechenov University), 119435 Moscow, Russia
| | - Luisa Ronga
- Université de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France.
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14
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James EI, Murphree TA, Vorauer C, Engen JR, Guttman M. Advances in Hydrogen/Deuterium Exchange Mass Spectrometry and the Pursuit of Challenging Biological Systems. Chem Rev 2021; 122:7562-7623. [PMID: 34493042 PMCID: PMC9053315 DOI: 10.1021/acs.chemrev.1c00279] [Citation(s) in RCA: 101] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
![]()
Solution-phase hydrogen/deuterium
exchange (HDX) coupled to mass
spectrometry (MS) is a widespread tool for structural analysis across
academia and the biopharmaceutical industry. By monitoring the exchangeability
of backbone amide protons, HDX-MS can reveal information about higher-order
structure and dynamics throughout a protein, can track protein folding
pathways, map interaction sites, and assess conformational states
of protein samples. The combination of the versatility of the hydrogen/deuterium
exchange reaction with the sensitivity of mass spectrometry has enabled
the study of extremely challenging protein systems, some of which
cannot be suitably studied using other techniques. Improvements over
the past three decades have continually increased throughput, robustness,
and expanded the limits of what is feasible for HDX-MS investigations.
To provide an overview for researchers seeking to utilize and derive
the most from HDX-MS for protein structural analysis, we summarize
the fundamental principles, basic methodology, strengths and weaknesses,
and the established applications of HDX-MS while highlighting new
developments and applications.
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Affiliation(s)
- Ellie I James
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Taylor A Murphree
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Clint Vorauer
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - John R Engen
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Miklos Guttman
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
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15
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Tang P, Tan Z, Ehamparanathan V, Ren T, Hoffman L, Du C, Song Y, Tao L, Lewandowski A, Ghose S, Li ZJ, Liu S. Optimization and kinetic modeling of interchain disulfide bond reoxidation of monoclonal antibodies in bioprocesses. MAbs 2021; 12:1829336. [PMID: 33031716 PMCID: PMC7577745 DOI: 10.1080/19420862.2020.1829336] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Disulfide bonds play a crucial role in folding and structural stabilization of monoclonal antibodies (mAbs). Disulfide bond reduction may happen during the mAb manufacturing process, resulting in low molecular weight species and possible failure to meet product specifications. Although many mitigation strategies have been developed to prevent disulfide reduction, to the best of our knowledge, reforming disulfide bonds from the reduced antibody in manufacturing has not previously been reported. Here, we explored a novel rescue strategy in the downstream process to repair the broken disulfide bonds via in-vitro redox reactions on Protein A resin. Redox conditions including redox pair (cysteine/cystine ratio), pH, temperature, and reaction time were examined to achieve high antibody purity and a high reaction rate. Under the optimal redox condition, >90% reduced antibody could be reoxidized to form an intact antibody on Protein A resin in an hour. In addition, this study showed high flexibility on the range of the intact mAb fraction in the initial reduced mAb sample (the lower limit of intact mAb faction could be 14% based on the data reported in this study). Furthermore, a kinetic model based on elementary oxidative reactions was constructed to help optimize the reoxidation conditions and to predict product purity. Together, the deep understanding of interchain disulfide bond reoxidation, combined with the predictive kinetic model, provided a good foundation to implement a rescue strategy to generate high-purity antibodies with substantial cost savings in manufacturing processes.
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Affiliation(s)
- Peifeng Tang
- Global Product Development and Supply, Bristol-Myers Squibb Company , Devens, MA, USA.,Department of Paper and Bioprocess Engineering, The State University of New York College of Environmental Science and Forestry , Syracuse, NY, USA
| | - Zhijun Tan
- Global Product Development and Supply, Bristol-Myers Squibb Company , Devens, MA, USA
| | - Vivekh Ehamparanathan
- Global Product Development and Supply, Bristol-Myers Squibb Company , Devens, MA, USA
| | - Tingwei Ren
- Global Product Development and Supply, Bristol-Myers Squibb Company , Devens, MA, USA
| | - Laurel Hoffman
- Global Product Development and Supply, Bristol-Myers Squibb Company , Pennington, NJ, USA
| | - Cheng Du
- Global Product Development and Supply, Bristol-Myers Squibb Company , Devens, MA, USA
| | - Yuanli Song
- Global Product Development and Supply, Bristol-Myers Squibb Company , Devens, MA, USA
| | - Li Tao
- Global Product Development and Supply, Bristol-Myers Squibb Company , Pennington, NJ, USA
| | - Angela Lewandowski
- Global Product Development and Supply, Bristol-Myers Squibb Company , Devens, MA, USA
| | - Sanchayita Ghose
- Global Product Development and Supply, Bristol-Myers Squibb Company , Devens, MA, USA
| | - Zheng Jian Li
- Global Product Development and Supply, Bristol-Myers Squibb Company , Devens, MA, USA
| | - Shijie Liu
- Department of Paper and Bioprocess Engineering, The State University of New York College of Environmental Science and Forestry , Syracuse, NY, USA
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16
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Zeng Y, Shinada K, Hano K, Sui L, Yang T, Li X, Himaki T. Effects of tris (2-carboxyethyl) phosphine hydrochloride treatment on porcine oocyte in vitro maturation and subsequent in vitro fertilized embryo developmental capacity. Theriogenology 2021; 162:32-41. [PMID: 33444914 DOI: 10.1016/j.theriogenology.2020.12.027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 12/27/2020] [Accepted: 12/30/2020] [Indexed: 12/23/2022]
Abstract
Oocyte in vitro maturation (IVM) is a crucial process that determines subsequent in vitro embryo production. The present study investigated the effects of the antioxidant tris (2-carboxyethyl) phosphine hydrochloride (TCEP-HCL) on the in vitro maturation of porcine oocytes and in vitro developmental competence of fertilized embryos. Oocytes were matured in IVM medium based on four concentration groups of TCEP-HCL (0, 50, 100, and 200 μM) treatment. 100 μM TCEP-HCL treatment significantly increased the oocyte first polar body extrusion rate, monospermy rate and subsequent in vitro fertilized embryo developmental capacity (cleavage rate, blastocyst formation rate, and blastocyst total cell number) compared to those in the control group. Furthermore, 100 μM TCEP-HCL treatment significantly reduced the levels of reactive oxygen species, significantly increased glutathione levels and mitochondrial content compared to those in the control group. Moreover, 100 μM TCEP-HCL treatment significantly decreased the oocyte apoptosis, blastocyst apoptosis compared to that in the controls. In summary, these results indicate that 100 μM TCEP-HCL treatment improves the quality and developmental capacity of in vitro-fertilized embryos by decreasing oxidative stress in porcine oocytes.
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Affiliation(s)
- Yiren Zeng
- Department of Agricultural and Environmental Science, Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan; State Key Laboratory for Conservation and Utilization of Subtropical Agro-bio Resources, Guangxi University, Nanning, Guangxi, 530004, China
| | - Kohei Shinada
- Department of Agricultural and Environmental Science, Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan
| | - Kazuki Hano
- Department of Agricultural and Environmental Science, Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan
| | - Lumin Sui
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bio Resources, Guangxi University, Nanning, Guangxi, 530004, China
| | - Ting Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bio Resources, Guangxi University, Nanning, Guangxi, 530004, China
| | - Xiangping Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bio Resources, Guangxi University, Nanning, Guangxi, 530004, China
| | - Takehiro Himaki
- Department of Agricultural and Environmental Science, Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan.
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17
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Sadiki A, Vaidya SR, Abdollahi M, Bhardwaj G, Dolan ME, Turna H, Arora V, Sanjeev A, Robinson TD, Koid A, Amin A, Zhou ZS. Site-specific conjugation of native antibody. Antib Ther 2020; 3:271-284. [PMID: 33644685 PMCID: PMC7906296 DOI: 10.1093/abt/tbaa027] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Traditionally, non-specific chemical conjugations, such as acylation of amines on lysine or alkylation of thiols on cysteines, are widely used; however, they have several shortcomings. First, the lack of site-specificity results in heterogeneous products and irreproducible processes. Second, potential modifications near the complementarity-determining region may reduce binding affinity and specificity. Conversely, site-specific methods produce well-defined and more homogenous antibody conjugates, ensuring developability and clinical applications. Moreover, several recent side-by-side comparisons of site-specific and stochastic methods have demonstrated that site-specific approaches are more likely to achieve their desired properties and functions, such as increased plasma stability, less variability in dose-dependent studies (particularly at low concentrations), enhanced binding efficiency, as well as increased tumor uptake. Herein, we review several standard and practical site-specific bioconjugation methods for native antibodies, i.e., those without recombinant engineering. First, chemo-enzymatic techniques, namely transglutaminase (TGase)-mediated transamidation of a conserved glutamine residue and glycan remodeling of a conserved asparagine N-glycan (GlyCLICK), both in the Fc region. Second, chemical approaches such as selective reduction of disulfides (ThioBridge) and N-terminal amine modifications. Furthermore, we list site-specific antibody–drug conjugates in clinical trials along with the future perspectives of these site-specific methods.
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Affiliation(s)
- Amissi Sadiki
- Department of Chemistry and Chemical Biology, Northeastern University Boston, Massachusetts 02115-5000, USA.,Barnett Institute of Chemical and Biological Analysis, Northeastern University Boston, Massachusetts 02115-5000, USA
| | - Shefali R Vaidya
- Department of Chemistry and Chemical Biology, Northeastern University Boston, Massachusetts 02115-5000, USA.,Barnett Institute of Chemical and Biological Analysis, Northeastern University Boston, Massachusetts 02115-5000, USA
| | - Mina Abdollahi
- Department of Chemistry and Chemical Biology, Northeastern University Boston, Massachusetts 02115-5000, USA.,Barnett Institute of Chemical and Biological Analysis, Northeastern University Boston, Massachusetts 02115-5000, USA
| | - Gunjan Bhardwaj
- Department of Chemistry and Chemical Biology, Northeastern University Boston, Massachusetts 02115-5000, USA.,Barnett Institute of Chemical and Biological Analysis, Northeastern University Boston, Massachusetts 02115-5000, USA
| | - Michael E Dolan
- Department of Chemistry and Chemical Biology, Northeastern University Boston, Massachusetts 02115-5000, USA.,Barnett Institute of Chemical and Biological Analysis, Northeastern University Boston, Massachusetts 02115-5000, USA.,Downstream Development, Biologics Process Development, Millennium Pharmaceuticals, Inc., (a wholly-owned subsidiary of Takeda Pharmaceuticals Company Limited), Cambridge, Massachusetts 02139, USA
| | - Harpreet Turna
- Department of Chemistry and Chemical Biology, Northeastern University Boston, Massachusetts 02115-5000, USA.,Barnett Institute of Chemical and Biological Analysis, Northeastern University Boston, Massachusetts 02115-5000, USA
| | - Varnika Arora
- Department of Chemistry and Chemical Biology, Northeastern University Boston, Massachusetts 02115-5000, USA.,Barnett Institute of Chemical and Biological Analysis, Northeastern University Boston, Massachusetts 02115-5000, USA
| | - Athul Sanjeev
- Department of Chemistry and Chemical Biology, Northeastern University Boston, Massachusetts 02115-5000, USA.,Barnett Institute of Chemical and Biological Analysis, Northeastern University Boston, Massachusetts 02115-5000, USA
| | - Timothy D Robinson
- Department of Chemistry and Chemical Biology, Northeastern University Boston, Massachusetts 02115-5000, USA.,Barnett Institute of Chemical and Biological Analysis, Northeastern University Boston, Massachusetts 02115-5000, USA
| | - Andrea Koid
- Department of Chemistry and Chemical Biology, Northeastern University Boston, Massachusetts 02115-5000, USA.,Barnett Institute of Chemical and Biological Analysis, Northeastern University Boston, Massachusetts 02115-5000, USA
| | - Aashka Amin
- Department of Chemistry and Chemical Biology, Northeastern University Boston, Massachusetts 02115-5000, USA.,Barnett Institute of Chemical and Biological Analysis, Northeastern University Boston, Massachusetts 02115-5000, USA
| | - Zhaohui Sunny Zhou
- Department of Chemistry and Chemical Biology, Northeastern University Boston, Massachusetts 02115-5000, USA.,Barnett Institute of Chemical and Biological Analysis, Northeastern University Boston, Massachusetts 02115-5000, USA
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18
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Bioinformatic and experimental evidence for suicidal and catalytic plant THI4s. Biochem J 2020; 477:2055-2069. [PMID: 32441748 DOI: 10.1042/bcj20200297] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 05/20/2020] [Accepted: 05/21/2020] [Indexed: 12/14/2022]
Abstract
Like fungi and some prokaryotes, plants use a thiazole synthase (THI4) to make the thiazole precursor of thiamin. Fungal THI4s are suicide enzymes that destroy an essential active-site Cys residue to obtain the sulfur atom needed for thiazole formation. In contrast, certain prokaryotic THI4s have no active-site Cys, use sulfide as sulfur donor, and are truly catalytic. The presence of a conserved active-site Cys in plant THI4s and other indirect evidence implies that they are suicidal. To confirm this, we complemented the Arabidopsistz-1 mutant, which lacks THI4 activity, with a His-tagged Arabidopsis THI4 construct. LC-MS analysis of tryptic peptides of the THI4 extracted from leaves showed that the active-site Cys was predominantly in desulfurated form, consistent with THI4 having a suicide mechanism in planta. Unexpectedly, transcriptome data mining and deep proteome profiling showed that barley, wheat, and oat have both a widely expressed canonical THI4 with an active-site Cys, and a THI4-like paralog (non-Cys THI4) that has no active-site Cys and is the major type of THI4 in developing grains. Transcriptomic evidence also indicated that barley, wheat, and oat grains synthesize thiamin de novo, implying that their non-Cys THI4s synthesize thiazole. Structure modeling supported this inference, as did demonstration that non-Cys THI4s have significant capacity to complement thiazole auxotrophy in Escherichia coli. There is thus a prima facie case that non-Cys cereal THI4s, like their prokaryotic counterparts, are catalytic thiazole synthases. Bioenergetic calculations show that, relative to suicide THI4s, such enzymes could save substantial energy during the grain-filling period.
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19
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Goerner-Hu X, Scott EL, Seeger T, Schneider O, Bitter JH. Reaction Stages of Feather Hydrolysis: Factors That Influence Availability for Enzymatic Hydrolysis and Cystine Conservation during Thermal Pressure Hydrolysis. BIOTECHNOL BIOPROC E 2020. [DOI: 10.1007/s12257-019-0351-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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20
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Mthembu SN, Sharma A, Albericio F, de la Torre BG. Breaking a Couple: Disulfide Reducing Agents. Chembiochem 2020; 21:1947-1954. [PMID: 32196882 DOI: 10.1002/cbic.202000092] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 03/19/2020] [Indexed: 01/20/2023]
Abstract
Cysteine is present in a large number of natural and synthetic (bio)molecules. Although the thiol side chain of Cys can be in a free form, in most cases it forms a disulfide bond either with a second Cys (bridge) or with another thiol, as in the case of protecting groups. Efficient reduction of these disulfide bridges is a requirement for many applications of Cys-containing molecules in the fields of chemistry and biochemistry. Here we review reducing methods for disulfide bonds, taking into consideration the solubility of the substrates when selecting the appropriate reducing reagent.
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Affiliation(s)
- Sinenhlanhla N Mthembu
- Peptide Science Laboratory, School of Chemistry and Physics, University of KwaZulu-Natal, Durban, 4001, South Africa.,KRISP, School of Laboratory of Medicine and Medical Sciences College of Health Sciences, University of KwaZulu-Natal Westville, Durban, 4001, South Africa
| | - Anamika Sharma
- Peptide Science Laboratory, School of Chemistry and Physics, University of KwaZulu-Natal, Durban, 4001, South Africa.,KRISP, School of Laboratory of Medicine and Medical Sciences College of Health Sciences, University of KwaZulu-Natal Westville, Durban, 4001, South Africa
| | - Fernando Albericio
- Peptide Science Laboratory, School of Chemistry and Physics, University of KwaZulu-Natal, Durban, 4001, South Africa.,Department of Organic Chemistry, University of Barcelona, Martí i Franqués 1-11, Barcelona, 08028, Spain.,CIBER-BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine IQAC, CSIC, Jordi Girona, Barcelona, 08028, Spain
| | - Beatriz G de la Torre
- KRISP, School of Laboratory of Medicine and Medical Sciences College of Health Sciences, University of KwaZulu-Natal Westville, Durban, 4001, South Africa
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21
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Wang D, Nowak C, Mason B, Katiyar A, Liu H. Analytical artifacts in characterization of recombinant monoclonal antibody therapeutics. J Pharm Biomed Anal 2020; 183:113131. [DOI: 10.1016/j.jpba.2020.113131] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 01/22/2020] [Accepted: 01/24/2020] [Indexed: 01/12/2023]
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22
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Tan Z, Ehamparanathan V, Ren T, Tang P, Hoffman L, Kuang J, Liu P, Huang C, Du C, Tao L, Chemmalil L, Lewandowski A, Ghose S, Li ZJ, Liu S. On-column disulfide bond formation of monoclonal antibodies during Protein A chromatography eliminates low molecular weight species and rescues reduced antibodies. MAbs 2020; 12:1829333. [PMID: 33016217 PMCID: PMC7577237 DOI: 10.1080/19420862.2020.1829333] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 08/13/2020] [Accepted: 09/14/2020] [Indexed: 12/13/2022] Open
Abstract
Disulfide bond reduction, which commonly occurs during monoclonal antibody (mAb) manufacturing processes, can result in a drug substance with high levels of low molecular weight (LMW) species that may fail release specifications because the drug's safety and the efficiency may be affected by the presence of this material. We previously studied disulfide reoxidation of mAbs and demonstrated that disulfide bonds could be reformed from the reduced antibody via redox reactions under an optimal redox condition on Protein A resin. The study here implements a redox system in a manufacturing setting to rescue the reduced mAb product and to further eliminate LMW issues in downstream processing. As such, we incorporate the optimized redox system as one of the wash buffers in Protein A chromatography to enable an on-column disulfide reoxidation to form intact antibody in vitro. Studies at laboratory scale (1 cm (ID) x 20 cm (Height), MabSelect SuRe LX) and pilot scale (30 cm (ID) x 20 cm (Height), MabSelect SuRe LX) were performed to demonstrate the effectiveness and robustness of disulfide formation with multiple mAbs using redox wash on Protein A columns. By applying this rescue strategy using ≤50 g/L-resin loading, the intact mAb purity was improved from <5% in the Protein A column load to >90% in the Protein A column elution with a product yield of >90%. Studies were also done to confirm that adding the redox wash has no negative impact on process yield or impurity removal or product quality. The rescued mAbs were confirmed to form complete interchain disulfide bonds, exhibiting comparable biophysical properties to the reference material. Furthermore, since the redox wash is followed by a bridging buffer wash before the final elution, no additional burden is involved in removing the redox components during the downstream steps. Due to its ease of implementation, significant product purity improvement, and minimal impact on other product quality attributes, we demonstrate that the on-column reoxidation using a redox system is a powerful, simple, and safe tool to recover reduced mAb during manufacturing. Moreover, the apparent benefits of using a high-pH redox wash may further drive the evolution of Protein A platform processes.
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Affiliation(s)
- Zhijun Tan
- Global Product Development and Supply, Bristol-Myers Squibb Company, Devens, MA, USA
| | - Vivekh Ehamparanathan
- Global Product Development and Supply, Bristol-Myers Squibb Company, Devens, MA, USA
| | - Tingwei Ren
- Global Product Development and Supply, Bristol-Myers Squibb Company, Devens, MA, USA
| | - Peifeng Tang
- Global Product Development and Supply, Bristol-Myers Squibb Company, Devens, MA, USA
- Department of Paper and Bioprocess Engineering, The State University of New York College of Environmental Science and Forestry, Syracuse, NY, USA
| | - Laurel Hoffman
- Global Product Development and Supply, Bristol-Myers Squibb Company, Pennington, NJ, USA
| | - June Kuang
- Global Product Development and Supply, Bristol-Myers Squibb Company, Devens, MA, USA
| | - Peiran Liu
- Global Product Development and Supply, Bristol-Myers Squibb Company, Pennington, NJ, USA
| | - Chao Huang
- Global Product Development and Supply, Bristol-Myers Squibb Company, Devens, MA, USA
| | - Cheng Du
- Global Product Development and Supply, Bristol-Myers Squibb Company, Devens, MA, USA
| | - Li Tao
- Global Product Development and Supply, Bristol-Myers Squibb Company, Pennington, NJ, USA
| | - Letha Chemmalil
- Global Product Development and Supply, Bristol-Myers Squibb Company, Devens, MA, USA
| | - Angela Lewandowski
- Global Product Development and Supply, Bristol-Myers Squibb Company, Devens, MA, USA
| | - Sanchayita Ghose
- Global Product Development and Supply, Bristol-Myers Squibb Company, Devens, MA, USA
| | - Zheng Jian Li
- Global Product Development and Supply, Bristol-Myers Squibb Company, Devens, MA, USA
| | - Shijie Liu
- Department of Paper and Bioprocess Engineering, The State University of New York College of Environmental Science and Forestry, Syracuse, NY, USA
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23
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Schöneich C. Thiyl Radical Reactions in the Chemical Degradation of Pharmaceutical Proteins. Molecules 2019; 24:E4357. [PMID: 31795282 PMCID: PMC6930596 DOI: 10.3390/molecules24234357] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 11/16/2019] [Accepted: 11/18/2019] [Indexed: 01/01/2023] Open
Abstract
Free radical pathways play a major role in the degradation of protein pharmaceuticals. Inspired by biochemical reactions carried out by thiyl radicals in various enzymatic processes, this review focuses on the role of thiyl radicals in pharmaceutical protein degradation through hydrogen atom transfer, electron transfer, and addition reactions. These processes can lead to the epimerization of amino acids, as well as the formation of various cleavage products and cross-links. Examples are presented for human insulin, human and mouse growth hormone, and monoclonal antibodies.
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Affiliation(s)
- Christian Schöneich
- Department of Pharmaceutical Chemistry, University of Kansas, 2093 Constant Avenue, Lawrence, KS 66047, USA
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24
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Horváth D, Taricska N, Keszei E, Stráner P, Farkas V, Tóth GK, Perczel A. Compactness of Protein Folds Alters Disulfide-Bond Reducibility by Three Orders of Magnitude: A Comprehensive Kinetic Case Study on the Reduction of Differently Sized Tryptophan Cage Model Proteins. Chembiochem 2019; 21:681-695. [PMID: 31475422 PMCID: PMC7079008 DOI: 10.1002/cbic.201900470] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Indexed: 12/12/2022]
Abstract
A new approach to monitor disulfide-bond reduction in the vicinity of aromatic cluster(s) has been derived by using the near-UV range (λ=266-293 nm) of electronic circular dichroism (ECD) spectra. By combining the results from NMR and ECD spectroscopy, the 3D fold characteristics and associated reduction rate constants (k) of E19_SS, which is a highly thermostable, disulfide-bond reinforced 39-amino acid long exenatide mimetic, and its N-terminally truncated derivatives have been determined under different experimental conditions. Single disulfide bond reduction of the E19_SS model (with an 18-fold excess of tris(2-carboxyethyl)phosphine, pH 7, 37 °C) takes hours, which is 20-30 times longer than that expected, and thus, would not reach completion by applying commonly used reduction protocols. It is found that structural, steric, and electrostatic factors influence the reduction rate, resulting in orders of magnitude differences in reduction half-lives (900>t1/2 >1 min) even for structurally similar, well-folded derivatives of a small model protein.
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Affiliation(s)
- Dániel Horváth
- Laboratory of Structural Chemistry and Biology and, MTA-ELTE Protein Modeling Research Group at the Institute of Chemistry, Eötvös Loránd University, 112, P. O. Box 32, 1518, Budapest, Hungary
| | - Nóra Taricska
- Laboratory of Structural Chemistry and Biology and, MTA-ELTE Protein Modeling Research Group at the Institute of Chemistry, Eötvös Loránd University, 112, P. O. Box 32, 1518, Budapest, Hungary
| | - Ernő Keszei
- Chemical Kinetics Laboratory, Institute of Chemistry, Eötvös Loránd University, 112, P. O. Box 32, 1518, Budapest, Hungary
| | - Pál Stráner
- Laboratory of Structural Chemistry and Biology and, MTA-ELTE Protein Modeling Research Group at the Institute of Chemistry, Eötvös Loránd University, 112, P. O. Box 32, 1518, Budapest, Hungary
| | - Viktor Farkas
- Laboratory of Structural Chemistry and Biology and, MTA-ELTE Protein Modeling Research Group at the Institute of Chemistry, Eötvös Loránd University, 112, P. O. Box 32, 1518, Budapest, Hungary
| | - Gábor K Tóth
- Department of Medical Chemistry, Faculty of General Medicine, University of Szeged, Szeged Dóm tér 8, H-6720, Szeged, Hungary
| | - András Perczel
- Laboratory of Structural Chemistry and Biology and, MTA-ELTE Protein Modeling Research Group at the Institute of Chemistry, Eötvös Loránd University, 112, P. O. Box 32, 1518, Budapest, Hungary
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25
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Melnikova DL, Skirda VD, Nesmelova IV. Effect of Reducing Agent TCEP on Translational Diffusion and Supramolecular Assembly in Aqueous Solutions of α-Casein. J Phys Chem B 2019; 123:2305-2315. [PMID: 30789730 DOI: 10.1021/acs.jpcb.8b12511] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The translational diffusion coefficient is highly sensitive to the size change of diffusing species and is ideally suited for the study of molecular association. Here, we used translational diffusion measurements by a pulsed-field gradient nuclear magnetic resonance (PFG NMR) technique to investigate the role of disulfide bonds in the formation of a supramolecular gel-like structure in the concentrated solution of α-casein. To reduce disulfide bonds, we added a commonly used reducing reagent tris(2-carboxyethyl)phosphine (TCEP) to α-casein solution. We found that the disruption of a disulfide bond Cys36-Cys40 in αs2-casein does not alter the translational diffusion or secondary structure of α-casein in dilute, 1 and 3% (wt %) solution. On the contrary, in concentrated, 15% (wt %) α-casein solution, in addition to the disruption of disulfide bonds, TCEP induced significant changes in gel properties. New long-lived intermolecular interactions formed, leading to the irreversible gel formation. While a few side reactions of TCEP (as well as other reducing agents, e.g., dithiothreitol) have been reported, this area is still understudied. Here, we provide new data on the side reaction of the reducing agent TCEP in concentrated protein solution, suggesting that at high protein concentrations TCEP should be used with caution.
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Affiliation(s)
- Daria L Melnikova
- Department of Physics , Kazan Federal University , Kazan 420011 , Russia
| | - Vladimir D Skirda
- Department of Physics , Kazan Federal University , Kazan 420011 , Russia
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26
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Wang J, Zhang W, Salter R, Lim HK. Reductive Desulfuration as an Important Tool in Detection of Small Molecule Modifications to Payload of Antibody Drug Conjugates. Anal Chem 2019; 91:2368-2375. [DOI: 10.1021/acs.analchem.8b05134] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Jianyao Wang
- Department of Drug Metabolism and Pharmacokinetics, Janssen Research & Development, Welsh & McKean Roads, Spring House, Pennsylvania 19477, United States
| | - Wei Zhang
- Department of Drug Metabolism and Pharmacokinetics, Janssen Research & Development, Welsh & McKean Roads, Spring House, Pennsylvania 19477, United States
| | - Rhys Salter
- Department of Drug Metabolism and Pharmacokinetics, Janssen Research & Development, Welsh & McKean Roads, Spring House, Pennsylvania 19477, United States
| | - Heng-Keang Lim
- Department of Drug Metabolism and Pharmacokinetics, Janssen Research & Development, Welsh & McKean Roads, Spring House, Pennsylvania 19477, United States
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27
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Reducing Complexity? Cysteine Reduction and S-Alkylation in Proteomic Workflows: Practical Considerations. Methods Mol Biol 2019; 1977:83-97. [PMID: 30980324 DOI: 10.1007/978-1-4939-9232-4_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Reduction and alkylation are common processing steps in sample preparation for qualitative and quantitative proteomic analyses. In principle, these steps mitigate the limitations resulting from the presence of disulfide bridges. There has been recurring debate in the proteomics community around their use, with concern over negative impacts that result from overalkylation (off-target, non-thiol sites) or incomplete reduction and/or S-alkylation of cysteine. This chapter integrates findings from a number of studies on different reduction and alkylation strategies, to guide users in experimental design for their optimal use in proteomic workflows.
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28
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Wang Y, Han L, Yuan N, Wang H, Li H, Liu J, Chen H, Zhang Q, Dong S. Traceless β-mercaptan-assisted activation of valinyl benzimidazolinones in peptide ligations. Chem Sci 2018; 9:1940-1946. [PMID: 29675240 PMCID: PMC5892131 DOI: 10.1039/c7sc04148a] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 01/04/2018] [Indexed: 12/27/2022] Open
Abstract
Peptidyl thioesters or their surrogates with C-terminal β-branched hydrophobic amino acid residues usually exhibit poor reactivities in ligation reactions. Thus, activation using exogenous additives is required to ensure an acceptable reaction efficiency. Herein, we report a traceless ligation at Val-Xaa sites under mild thiol additive-free reaction conditions, whereby the introduction of β-mercaptan on the C-terminal valine residue effectively activates the otherwise unreactive N-acyl-benzimidazolinone (Nbz), and enables the use of a one-pot ligation-desulfurization strategy to generate the desired peptide products. The orthogonality between β-thiovaline-Nbz and a conventional alkyl thioester, as well as the convenient access to the former from readily available penicillamine, also allowed expedited assembly of the peptidic hormone β-LPH and hPTH analogues, based on a kinetically controlled one-pot three-segment ligation and desulfurization strategy.
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Affiliation(s)
- Yinglu Wang
- State Key Laboratory of Natural and Biomimetic Drugs , Department of Chemical Biology , School of Pharmaceutical Sciences , Peking University , Beijing 100191 , China .
| | - Lin Han
- State Key Laboratory of Natural and Biomimetic Drugs , Department of Chemical Biology , School of Pharmaceutical Sciences , Peking University , Beijing 100191 , China .
| | - Ning Yuan
- State Key Laboratory of Natural and Biomimetic Drugs , Department of Chemical Biology , School of Pharmaceutical Sciences , Peking University , Beijing 100191 , China .
| | - Hanxuan Wang
- State Key Laboratory of Natural and Biomimetic Drugs , Department of Chemical Biology , School of Pharmaceutical Sciences , Peking University , Beijing 100191 , China .
| | - Hongxing Li
- State Key Laboratory of Natural and Biomimetic Drugs , Department of Chemical Biology , School of Pharmaceutical Sciences , Peking University , Beijing 100191 , China .
| | - Jinrong Liu
- State Key Laboratory of Natural and Biomimetic Drugs , Department of Chemical Biology , School of Pharmaceutical Sciences , Peking University , Beijing 100191 , China .
| | - Huan Chen
- Department of Chemistry , University at Albany , Albany , New York 12222 , USA .
| | - Qiang Zhang
- Department of Chemistry , University at Albany , Albany , New York 12222 , USA .
| | - Suwei Dong
- State Key Laboratory of Natural and Biomimetic Drugs , Department of Chemical Biology , School of Pharmaceutical Sciences , Peking University , Beijing 100191 , China .
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29
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Photodegradation Pathways of Protein Disulfides: Human Growth Hormone. Pharm Res 2017; 34:2756-2778. [DOI: 10.1007/s11095-017-2256-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 09/05/2017] [Indexed: 11/25/2022]
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30
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Baumruck AC, Tietze D, Stark A, Tietze AA. Reactions of Sulfur-Containing Organic Compounds and Peptides in 1-Ethyl-3-methyl-imidazolium Acetate. J Org Chem 2017. [DOI: 10.1021/acs.joc.7b01272] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Andreas C. Baumruck
- Clemens-Schöpf
Institute of Organic Chemistry and Biochemistry, Darmstadt University of Technology, Alarich-Weiss Str. 4, 64287 Darmstadt, Germany
| | - Daniel Tietze
- Eduard-Zintl-Institute
of Inorganic and Physical Chemistry, Darmstadt Univeristy of Technology, Alarich-Weiss-Str. 4, D-64287 Darmstadt, Germany
| | - Annegret Stark
- Chemical
Engineering, University of KwaZulu-Natal, 238 Mazisi Kunene Rd, Glenwood, Durban 4001, South Africa
| | - Alesia A. Tietze
- Clemens-Schöpf
Institute of Organic Chemistry and Biochemistry, Darmstadt University of Technology, Alarich-Weiss Str. 4, 64287 Darmstadt, Germany
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31
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Burke MC, Mirokhin YA, Tchekhovskoi DV, Markey SP, Heidbrink Thompson J, Larkin C, Stein SE. The Hybrid Search: A Mass Spectral Library Search Method for Discovery of Modifications in Proteomics. J Proteome Res 2017; 16:1924-1935. [DOI: 10.1021/acs.jproteome.6b00988] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Meghan C. Burke
- Mass
Spectrometry Data Center, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899, United States
| | - Yuri A. Mirokhin
- Mass
Spectrometry Data Center, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899, United States
| | - Dmitrii V. Tchekhovskoi
- Mass
Spectrometry Data Center, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899, United States
| | - Sanford P. Markey
- Mass
Spectrometry Data Center, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899, United States
| | - Jenny Heidbrink Thompson
- Analytical
Sciences, MedImmune LLC, One MedImmune Way, Gaithersburg, Maryland 20878, United States
| | - Christopher Larkin
- Analytical
Sciences, MedImmune LLC, One MedImmune Way, Gaithersburg, Maryland 20878, United States
| | - Stephen E. Stein
- Mass
Spectrometry Data Center, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899, United States
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32
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Kitzig S, Rück-Braun K. Synthesis of hemithioindigo-based chromopeptides by using the Tmb auxiliary in native chemical ligation studies. J Pept Sci 2017; 23:567-573. [DOI: 10.1002/psc.3001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Revised: 02/23/2017] [Accepted: 03/06/2017] [Indexed: 01/08/2023]
Affiliation(s)
- S. Kitzig
- Institut für Chemie, Technische Universität Berlin; Str. des 17. Juni 135 10623 Berlin Germany
| | - K. Rück-Braun
- Institut für Chemie, Technische Universität Berlin; Str. des 17. Juni 135 10623 Berlin Germany
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33
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Gerke C, Ebbesen MF, Jansen D, Boden S, Freichel T, Hartmann L. Sequence-Controlled Glycopolymers via Step-Growth Polymerization of Precision Glycomacromolecules for Lectin Receptor Clustering. Biomacromolecules 2017; 18:787-796. [PMID: 28117986 DOI: 10.1021/acs.biomac.6b01657] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A versatile approach for the synthesis of sequence-controlled multiblock copolymers, using a combination of solid phase synthesis and step-growth polymerization by photoinduced thiol-ene coupling (TEC) is presented. Following this strategy, a series of sequence-controlled glycopolymers is derived from the polymerization of a hydrophilic spacer macromonomer and different glycomacromonomers bearing between one to five α-d-Mannose (Man) ligands. Through the solid phase assembly of the macromonomers, the number and positioning of spacer and sugar moieties is controlled and translates into the sequence-control of the final polymer. A maximum M̅n of 16 kDa, corresponding to a X̅n of 10, for the applied macromonomers is accessible with optimized polymerization conditions. The binding behavior of the resulting multiblock glycopolymers toward the model lectin Concanavalin A (ConA) is studied via turbidity assays and surface plasmon resonance (SPR) measurements, comparing the ability of precision glycomacromolecules and glycopolymers to bind to and cross-link ConA in dependence of the number of sugar moieties and overall molecular weight. The results show that there is a clear correlation between number of Man ligands and Con A binding and clustering, whereas the length of the glycooligomer- or polymer backbone seems to have no effect.
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Affiliation(s)
- Christoph Gerke
- Institute of Organic and Macromolecular Chemistry, Heinrich-Heine-University Düsseldorf , Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Morten F Ebbesen
- Institute of Organic and Macromolecular Chemistry, Heinrich-Heine-University Düsseldorf , Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Dennis Jansen
- Institute of Organic and Macromolecular Chemistry, Heinrich-Heine-University Düsseldorf , Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Sophia Boden
- Institute of Organic and Macromolecular Chemistry, Heinrich-Heine-University Düsseldorf , Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Tanja Freichel
- Institute of Organic and Macromolecular Chemistry, Heinrich-Heine-University Düsseldorf , Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Laura Hartmann
- Institute of Organic and Macromolecular Chemistry, Heinrich-Heine-University Düsseldorf , Universitätsstraße 1, 40225 Düsseldorf, Germany
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34
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Grigoryan H, Edmands W, Lu SS, Yano Y, Regazzoni L, Iavarone AT, Williams ER, Rappaport SM. Adductomics Pipeline for Untargeted Analysis of Modifications to Cys34 of Human Serum Albumin. Anal Chem 2016; 88:10504-10512. [PMID: 27684351 PMCID: PMC5555296 DOI: 10.1021/acs.analchem.6b02553] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
An important but understudied class of human exposures is comprised of reactive electrophiles that cannot be measured in vivo because they are short-lived. An avenue for assessing these meaningful exposures focuses on adducts from reactions with nucleophilic loci of blood proteins, particularly Cys34 of human serum albumin, which is the dominant scavenger of reactive electrophiles in serum. We developed an untargeted analytical scheme and bioinformatics pipeline for detecting, quantitating, and annotating Cys34 adducts in tryptic digests of human serum/plasma. The pipeline interrogates tandem mass spectra to find signatures of the Cys34-containing peptide, obtains accurate masses of putative adducts, quantitates adduct levels relative to a "housekeeping peptide", and annotates modifications based on a combination of retention time, accurate mass, elemental composition, and database searches. We used the adductomics pipeline to characterize 43 adduct features in archived plasma from healthy human subjects and found several that were highly associated with smoking status, race, and other covariates. Since smoking is a strong risk factor for cancer and cardiovascular disease, our ability to discover adducts that distinguish smokers from nonsmokers with untargeted adductomics indicates that the pipeline is suitable for use in epidemiologic studies. In fact, adduct features were both positively and negatively associated with smoking, indicating that some adducts arise from reactions between Cys34 and constituents of cigarette smoke (e.g., ethylene oxide and acrylonitrile) while others (Cys34 oxidation products and disulfides) appear to reflect alterations in the serum redox state that resulted in reduced adduct levels in smokers.
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Affiliation(s)
- Hasmik Grigoryan
- School of Public Health, University of California, Berkeley, California 94720-7356, United States
| | - William Edmands
- School of Public Health, University of California, Berkeley, California 94720-7356, United States
| | - Sixin S. Lu
- School of Public Health, University of California, Berkeley, California 94720-7356, United States
| | - Yukiko Yano
- School of Public Health, University of California, Berkeley, California 94720-7356, United States
| | - Luca Regazzoni
- School of Public Health, University of California, Berkeley, California 94720-7356, United States
| | - Anthony T. Iavarone
- California Institute for Quantitative Biosciences, University of California, Berkeley, California 94720, United States
| | - Evan R. Williams
- College of Chemistry, University of California, Berkeley, California 94720, United States
| | - Stephen M. Rappaport
- School of Public Health, University of California, Berkeley, California 94720-7356, United States
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35
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Comparison of Protein N-Homocysteinylation in Rat Plasma under Elevated Homocysteine Using a Specific Chemical Labeling Method. Molecules 2016; 21:molecules21091195. [PMID: 27617989 PMCID: PMC5292613 DOI: 10.3390/molecules21091195] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 09/02/2016] [Accepted: 09/05/2016] [Indexed: 11/30/2022] Open
Abstract
Elevated blood concentrations of homocysteine have been well established as a risk factor for cardiovascular diseases and neuropsychiatric diseases, yet the etiologic relationship of homocysteine to these disorders remains poorly understood. Protein N-homocysteinylation has been hypothesized as a contributing factor; however, it has not been examined globally owing to the lack of suitable detection methods. We recently developed a selective chemical method to label N-homocysteinylated proteins with a biotin-aldehyde tag followed by Western blotting analysis, which was further optimized in this study. We then investigated the variation of protein N-homocysteinylation in plasma from rats on a vitamin B12 deficient diet. Elevated “total homocysteine” concentrations were determined in rats with a vitamin B12 deficient diet. Correspondingly, overall levels of plasma protein N-homocysteinylation displayed an increased trend, and furthermore, more pronounced and statistically significant changes (e.g., 1.8-fold, p-value: 0.03) were observed for some individual protein bands. Our results suggest that, as expected, a general metabolic correlation exists between “total homocysteine” and N-homocysteinylation, although other factors are involved in homocysteine/homocysteine thiolactone metabolism, such as the transsulfuration of homocysteine by cystathionine β-synthase or the hydrolysis of homocysteine thiolactone by paraoxonase 1 (PON1), may play more significant or direct roles in determining the level of N-homocysteinylation.
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36
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Bayer M, König S. Abundant cysteine side reactions in traditional buffers interfere with the analysis of posttranslational modifications and protein quantification - How to compromise. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2016; 30:1823-1828. [PMID: 27426460 DOI: 10.1002/rcm.7613] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 05/17/2016] [Accepted: 05/20/2016] [Indexed: 06/06/2023]
Affiliation(s)
- Malte Bayer
- Core Unit Proteomics, Interdisciplinary Center for Clinical Research, Medical Faculty, University of Münster, Germany
| | - Simone König
- Core Unit Proteomics, Interdisciplinary Center for Clinical Research, Medical Faculty, University of Münster, Germany
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37
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Nickel-pincer cofactor biosynthesis involves LarB-catalyzed pyridinium carboxylation and LarE-dependent sacrificial sulfur insertion. Proc Natl Acad Sci U S A 2016; 113:5598-603. [PMID: 27114550 DOI: 10.1073/pnas.1600486113] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The lactate racemase enzyme (LarA) of Lactobacillus plantarum harbors a (SCS)Ni(II) pincer complex derived from nicotinic acid. Synthesis of the enzyme-bound cofactor requires LarB, LarC, and LarE, which are widely distributed in microorganisms. The functions of the accessory proteins are unknown, but the LarB C terminus resembles aminoimidazole ribonucleotide carboxylase/mutase, LarC binds Ni and could act in Ni delivery or storage, and LarE is a putative ATP-using enzyme of the pyrophosphatase-loop superfamily. Here, we show that LarB carboxylates the pyridinium ring of nicotinic acid adenine dinucleotide (NaAD) and cleaves the phosphoanhydride bond to release AMP. The resulting biscarboxylic acid intermediate is transformed into a bisthiocarboxylic acid species by two single-turnover reactions in which sacrificial desulfurization of LarE converts its conserved Cys176 into dehydroalanine. Our results identify a previously unidentified metabolic pathway from NaAD using unprecedented carboxylase and sulfur transferase reactions to form the organic component of the (SCS)Ni(II) pincer cofactor of LarA. In species where larA is absent, this pathway could be used to generate a pincer complex in other enzymes.
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38
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Gui Y, Qiu L, Li Y, Li H, Dong S. Internal Activation of Peptidyl Prolyl Thioesters in Native Chemical Ligation. J Am Chem Soc 2016; 138:4890-9. [DOI: 10.1021/jacs.6b01202] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Yue Gui
- State
Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical
Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
| | - Lingqi Qiu
- State
Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical
Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
| | - Yaohao Li
- State
Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical
Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
| | - Hongxing Li
- State
Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical
Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
| | - Suwei Dong
- State
Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical
Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
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39
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Ducret A, Kux van Geijtenbeek S, Röder D, Simon S, Chin D, Berrera M, Gruenbaum L, Ji C, Cutler P. Identification of six cell surface proteins for specific liver targeting. Proteomics Clin Appl 2016; 9:651-61. [PMID: 26097162 DOI: 10.1002/prca.201400194] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 03/27/2015] [Accepted: 06/08/2015] [Indexed: 01/09/2023]
Abstract
PURPOSE Cell surface proteins are the primary means for a cell to sense and interact with its environment and their dysregulation has been linked to numerous diseases. In particular, the identification of proteins specific to a single tissue type or to a given disease phenotype may enable the characterization of novel therapeutic targets. We tested here the feasibility of a cell surface proteomics approach to identify pertinent markers directly in a clinically relevant tissue. EXPERIMENTAL DESIGN We analyzed the cell surface proteome of freshly isolated primary heptatocytes using a glycocapture-specific approach combined with a robust bioinformatics filtering. RESULTS Using primary lung epithelial cell cultures as negative controls, we identified 32 hepatocyte-specific cell surface proteins candidates. We used mRNA expression to select six markers that may provide adequate specificity for targeting therapeutics to the liver. CONCLUSIONS AND CLINICAL RELEVANCE We demonstrate the feasibility and the importance of conducting such studies directly in a clinically relevant tissue. In particular, the cell surface proteome of freshly isolated hepatocytes differed substantially from cultured cell lines.
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Affiliation(s)
- Axel Ducret
- Translational Technologies and Bioinformatics, Pharmaceutical Sciences, Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche AG, Basel, Switzerland
| | - Sabine Kux van Geijtenbeek
- Translational Technologies and Bioinformatics, Pharmaceutical Sciences, Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche AG, Basel, Switzerland
| | - Daniel Röder
- Translational Technologies and Bioinformatics, Pharmaceutical Sciences, Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche AG, Basel, Switzerland
| | - Sandrine Simon
- Drug Disposition and Safety, Pharmaceutical Sciences, Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche AG, Basel, Switzerland
| | - Daniel Chin
- Translational Technologies and Bioinformatics, Pharmaceutical Sciences, Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche AG, Basel, Switzerland
| | - Marco Berrera
- Translational Technologies and Bioinformatics, Pharmaceutical Sciences, Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche AG, Basel, Switzerland
| | - Lore Gruenbaum
- Translational Medicine - Infectious Diseases, Pharma Research and Early Development (pRED), Roche Innovation Center New York, New York, NY, USA
| | - Changhua Ji
- External Alliances and Portfolio Management, Roche Pharma Research and Early Development (pRED), Roche Innovation Center Shanghai, Pudong, Shanghai, P. R. China
| | - Paul Cutler
- Translational Technologies and Bioinformatics, Pharmaceutical Sciences, Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche AG, Basel, Switzerland
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40
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Mildly acidic conditions eliminate deamidation artifact during proteolysis: digestion with endoprotease Glu-C at pH 4.5. Amino Acids 2016; 48:1059-1067. [PMID: 26748652 DOI: 10.1007/s00726-015-2166-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 12/25/2015] [Indexed: 10/22/2022]
Abstract
Common yet often overlooked, deamidation of peptidyl asparagine (Asn or N) generates aspartic acid (Asp or D) or isoaspartic acid (isoAsp or isoD). Being a spontaneous, non-enzymatic protein post-translational modification, deamidation artifact can be easily introduced during sample preparation, especially proteolysis where higher-order structures are removed. This artifact not only complicates the analysis of bona fide deamidation but also affects a wide range of chemical and enzymatic processes; for instance, the newly generated Asp and isoAsp residues may block or introduce new proteolytic sites, and also convert one Asn peptide into multiple species that affect quantification. While the neutral to mildly basic conditions for common proteolysis favor deamidation, mildly acidic conditions markedly slow down the process. Unlike other commonly used endoproteases, Glu-C remains active under mildly acid conditions. As such, as demonstrated herein, deamidation artifact during proteolysis was effectively eliminated by simply performing Glu-C digestion at pH 4.5 in ammonium acetate, a volatile buffer that is compatible with mass spectrometry. Moreover, nearly identical sequence specificity was observed at both pH's (8.0 for ammonium bicarbonate), rendering Glu-C as effective at pH 4.5. In summary, this method is generally applicable for protein analysis as it requires minimal sample preparation and uses the readily available Glu-C protease.
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41
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Dery S, Reddy PS, Dery L, Mousa R, Dardashti RN, Metanis N. Insights into the deselenization of selenocysteine into alanine and serine. Chem Sci 2015; 6:6207-6212. [PMID: 30090236 PMCID: PMC6054048 DOI: 10.1039/c5sc02528a] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 08/06/2015] [Indexed: 12/21/2022] Open
Abstract
The deselenization of selenocysteine selectively removes the selenol group to give alanine under anaerobic conditions or serine under aerobic conditions (oxygen saturation).
The development of native chemical ligation coupled with desulfurization has allowed ligation at several new ligation junctions. However, desulfurization also converts all cysteine residues in the protein sequence into alanine. Deselenization of selenocysteine, in contrast, selectively removes the selenol group to give alanine in the presence of unprotected cysteines. In this study we shed more light onto the deselenization mechanism of selenocysteine to alanine and provide optimized conditions for the reaction. The deselenization can be accomplished in one minute under anaerobic conditions to give alanine. Under aerobic conditions (oxygen saturation), selenocysteine is converted into serine.
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Affiliation(s)
- Shahar Dery
- Institute of Chemistry , The Hebrew University of Jerusalem , Jerusalem 91904 , Israel .
| | - Post Sai Reddy
- Institute of Chemistry , The Hebrew University of Jerusalem , Jerusalem 91904 , Israel .
| | - Linoy Dery
- Institute of Chemistry , The Hebrew University of Jerusalem , Jerusalem 91904 , Israel .
| | - Reem Mousa
- Institute of Chemistry , The Hebrew University of Jerusalem , Jerusalem 91904 , Israel .
| | | | - Norman Metanis
- Institute of Chemistry , The Hebrew University of Jerusalem , Jerusalem 91904 , Israel .
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42
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Chumsae C, Hossler P, Raharimampionona H, Zhou Y, McDermott S, Racicot C, Radziejewski C, Zhou ZS. When Good Intentions Go Awry: Modification of a Recombinant Monoclonal Antibody in Chemically Defined Cell Culture by Xylosone, an Oxidative Product of Ascorbic Acid. Anal Chem 2015; 87:7529-34. [DOI: 10.1021/acs.analchem.5b00801] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Chris Chumsae
- Protein
Analytics, Process Sciences Department, AbbVie Bioresearch Center, Worcester, Massachusetts 01605, United States
- Barnett
Institute of Chemical and Biological Analysis, Department of Chemistry
and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Patrick Hossler
- Cell
Culture, Process Sciences Department, AbbVie Bioresearch Center, Worcester, Massachusetts 01605, United States
| | - Haly Raharimampionona
- Protein
Analytics, Process Sciences Department, AbbVie Bioresearch Center, Worcester, Massachusetts 01605, United States
| | - Yu Zhou
- Protein
Analytics, Process Sciences Department, AbbVie Bioresearch Center, Worcester, Massachusetts 01605, United States
| | - Sean McDermott
- Cell
Culture, Process Sciences Department, AbbVie Bioresearch Center, Worcester, Massachusetts 01605, United States
| | - Chris Racicot
- Cell
Culture, Process Sciences Department, AbbVie Bioresearch Center, Worcester, Massachusetts 01605, United States
| | - Czeslaw Radziejewski
- Protein
Analytics, Process Sciences Department, AbbVie Bioresearch Center, Worcester, Massachusetts 01605, United States
| | - Zhaohui Sunny Zhou
- Barnett
Institute of Chemical and Biological Analysis, Department of Chemistry
and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
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43
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Campeciño JO, Dudycz LW, Tumelty D, Berg V, Cabelli DE, Maroney MJ. A Semisynthetic Strategy Leads to Alteration of the Backbone Amidate Ligand in the NiSOD Active Site. J Am Chem Soc 2015; 137:9044-52. [PMID: 26135142 DOI: 10.1021/jacs.5b03629] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Computational investigations have implicated the amidate ligand in nickel superoxide dismutase (NiSOD) in stabilizing Ni-centered redox catalysis and in preventing cysteine thiolate ligand oxidation. To test these predictions, we have used an experimental approach utilizing a semisynthetic scheme that employs native chemical ligation of a pentapeptide (HCDLP) to recombinant S. coelicolor NiSOD lacking these N-terminal residues, NΔ5-NiSOD. Wild-type enzyme produced in this manner exhibits the characteristic spectral properties of recombinant WT-NiSOD and is as catalytically active. The semisynthetic scheme was also employed to construct a variant where the amidate ligand was converted to a secondary amine, H1*-NiSOD, a novel strategy that retains a backbone N-donor atom. The H1*-NiSOD variant was found to have only ∼1% of the catalytic activity of the recombinant wild-type enzyme, and had altered spectroscopic properties. X-ray absorption spectroscopy reveals a four-coordinate planar site with N2S2-donor ligands, consistent with electronic absorption spectroscopic results indicating that the Ni center in H1*-NiSOD is mostly reduced in the as-isolated sample, as opposed to 50:50 Ni(II)/Ni(III) mixture that is typical for the recombinant wild-type enzyme. The EPR spectrum of as-isolated H1*-NiSOD accounts for ∼11% of the Ni in the sample and is similar to WT-NiSOD, but more axial, with gz < gx,y. (14)N-hyperfine is observed on gz, confirming the addition of the apical histidine ligand in the Ni(III) complex. The altered electronic properties and implications for redox catalysis are discussed in light of predictions based on synthetic and computational models.
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Affiliation(s)
- Julius O Campeciño
- †Department of Chemistry University of Massachusetts, Amherst, Massachusetts 01003, United States
| | - Lech W Dudycz
- ‡Lex Company Research Lab, Phoenix Park, 2 Shaker Road, Suite D 106, Shirley, Massachusetts 01464, United States
| | - David Tumelty
- §New England Peptide, 65 Zub Lane, Gardner, Massachusetts 01440, United States
| | - Volker Berg
- †Department of Chemistry University of Massachusetts, Amherst, Massachusetts 01003, United States
| | - Diane E Cabelli
- ∥Department of Chemistry, Brookhaven National Laboratory, Building 555A, P.O. Box 5000 Upton, New York 11973, United States
| | - Michael J Maroney
- †Department of Chemistry University of Massachusetts, Amherst, Massachusetts 01003, United States
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44
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Koniev O, Wagner A. Developments and recent advancements in the field of endogenous amino acid selective bond forming reactions for bioconjugation. Chem Soc Rev 2015; 44:5495-551. [PMID: 26000775 DOI: 10.1039/c5cs00048c] [Citation(s) in RCA: 391] [Impact Index Per Article: 43.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Bioconjugation methodologies have proven to play a central enabling role in the recent development of biotherapeutics and chemical biology approaches. Recent endeavours in these fields shed light on unprecedented chemical challenges to attain bioselectivity, biocompatibility, and biostability required by modern applications. In this review the current developments in various techniques of selective bond forming reactions of proteins and peptides were highlighted. The utility of each endogenous amino acid-selective conjugation methodology in the fields of biology and protein science has been surveyed with emphasis on the most relevant among reported transformations; selectivity and practical use have been discussed.
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Affiliation(s)
- Oleksandr Koniev
- Laboratory of Functional Chemo-Systems (UMR 7199), Labex Medalis, University of Strasbourg, 74 Route du Rhin, 67401 Illkirch-Graffenstaden, France.
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45
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Adamczyk J, Bal W, Krężel A. Coordination properties of dithiobutylamine (DTBA), a newly introduced protein disulfide reducing agent. Inorg Chem 2014; 54:596-606. [PMID: 25531180 DOI: 10.1021/ic5025026] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The acid-base properties and metal-binding abilities of (2S)-2-amino-1,4-dimercaptobutane, otherwise termed dithiobutylamine (DTBA), which is a newly introduced reagent useful for reducing protein and peptide disulfides, were studied in solution using potentiometry, (1)H NMR spectroscopy, spectropolarimetry, and UV-vis spectroscopy. The list of metal ions studied here includes Zn(II), Cd(II), Ni(II), Co(II), and Cu(I). We found that DTBA forms specific and very stable polynuclear and mononuclear complexes with all of these metal ions using both of its sulfur donors. DTBA forms complexes more stable than those of the commonly used disulfide reducing agent DTT, giving it more interference capacity in studies of metal binding in thiol-containing biomolecules. The ability of DTBA to strongly bind metal ions is reflected in its limited properties as a thiol protectant in their presence, which is manifested through slower disulfide reduction kinetics. We found that this effect correlated with the stabilities of the complexes. Additionally, the reducing properties of DTBA toward MMTS-modified papain (MMTS = S-methylmethanethiosulfonate) were also significantly affected by the investigated metal ions. In this case, however, electrostatic interactions and stereospecific effects, rather than metal-binding abilities, were found to be responsible for the reduced protective properties of DTBA. Despite its limitations, a high affinity toward metal ions makes DTBA an attractive agent in competition studies with metalloproteins.
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Affiliation(s)
- Justyna Adamczyk
- Laboratory of Chemical Biology, Faculty of Biotechnology, University of Wroclaw , Joliot-Curie 14a, 50-383 Wroclaw, Poland
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46
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Duclos RI, Cleary DC, Catcott KC, Zhou ZS. Synthesis and characterization of Se-adenosyl-L-selenohomocysteine selenoxide. J Sulphur Chem 2014; 36:135-144. [PMID: 26005494 DOI: 10.1080/17415993.2014.979173] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Selenium is an essential micronutrient in humans due to the important roles of the selenocysteine-containing selenoproteins. Organoselenium metabolites are generally found to be substrates for the biochemical pathways of their sulfur analogs, and the redox chemistry of selenomethionine and some other metabolites have been previously reported. We now report the first synthesis and characterization of Se-adenosylselenohomocysteine selenoxide (SeAHO) prepared via hydrogen peroxide oxidation of Se-adenosylselenohomocysteine (SeAH). The selenoxide SeAHO, in contrast to its corresponding sulfoxide S-adenosylhomocysteine (SAHO), can form hydrate, has an electrostatic interaction between the α-amino acid moiety and the highly polar selenoxide functional group, and readily oxidizes glutathione (GSH) and cysteine thiols.
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Affiliation(s)
- Richard I Duclos
- Department of Pharmaceutical Sciences, 140 The Fenway Bldg., Room 206, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115-5000, Tel: +1 617 373 3163
| | - Dillon C Cleary
- Department of Chemistry and Chemical Biology, Hurtig Hall, Room 102, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115-5000, Tel: +1 617 373 2800
| | - Kalli C Catcott
- Department of Chemistry and Chemical Biology, Hurtig Hall, Room 102, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115-5000, Tel: +1 617 373 2800
| | - Zhaohui Sunny Zhou
- Department of Chemistry and Chemical Biology, Hurtig Hall, Room 102, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115-5000, Tel: +1 617 373 2800
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47
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Chumsae C, Zhou LL, Shen Y, Wohlgemuth J, Fung E, Burton R, Radziejewski C, Zhou ZS. Discovery of a chemical modification by citric acid in a recombinant monoclonal antibody. Anal Chem 2014; 86:8932-6. [PMID: 25136741 PMCID: PMC4165448 DOI: 10.1021/ac502179m] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 08/19/2014] [Indexed: 01/07/2023]
Abstract
Recombinant therapeutic monoclonal antibodies exhibit a high degree of heterogeneity that can arise from various post-translational modifications. The formulation for a protein product is to maintain a specific pH and to minimize further modifications. Generally Recognized as Safe (GRAS), citric acid is commonly used for formulation to maintain a pH at a range between 3 and 6 and is generally considered chemically inert. However, as we reported herein, citric acid covalently modified a recombinant monoclonal antibody (IgG1) in a phosphate/citrate-buffered formulation at pH 5.2 and led to the formation of so-called "acidic species" that showed mass increases of 174 and 156 Da, respectively. Peptide mapping revealed that the modification occurred at the N-terminus of the light chain. Three additional antibodies also showed the same modification but displayed different susceptibilities of the N-termini of the light chain, heavy chain, or both. Thus, ostensibly unreactive excipients under certain conditions may increase heterogeneity and acidic species in formulated recombinant monoclonal antibodies. By analogy, other molecules (e.g., succinic acid) with two or more carboxylic acid groups and capable of forming an anhydride may exhibit similar reactivities. Altogether, our findings again reminded us that it is prudent to consider formulations as a potential source for chemical modifications and product heterogeneity.
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Affiliation(s)
- Chris Chumsae
- Protein
Analytics, Process Sciences, AbbVie Bioresearch
Center, Worcester, Massachusetts 01605, United States
- Barnett
Institute of Chemical and Biological Analysis, Department of Chemistry
and Chemical Biology, Northeastern University, Boston, Massachusetts 02115-5000, United States
| | - Liqiang Lisa Zhou
- Protein
Analytics, Process Sciences, AbbVie Bioresearch
Center, Worcester, Massachusetts 01605, United States
| | - Yang Shen
- Protein
Analytics, Process Sciences, AbbVie Bioresearch
Center, Worcester, Massachusetts 01605, United States
| | - Jessica Wohlgemuth
- NBE
Analytical Research and Development, AbbVie, Ludwigshafen 67061, Germany
| | - Emma Fung
- Biologics, AbbVie
Bioresearch Center, Worcester, Massachusetts 01605, United States
| | - Randall Burton
- Protein
Analytics, Process Sciences, AbbVie Bioresearch
Center, Worcester, Massachusetts 01605, United States
| | - Czeslaw Radziejewski
- Protein
Analytics, Process Sciences, AbbVie Bioresearch
Center, Worcester, Massachusetts 01605, United States
| | - Zhaohui Sunny Zhou
- Barnett
Institute of Chemical and Biological Analysis, Department of Chemistry
and Chemical Biology, Northeastern University, Boston, Massachusetts 02115-5000, United States
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48
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Klaene JJ, Ni W, Alfaro JF, Zhou ZS. Detection and quantitation of succinimide in intact protein via hydrazine trapping and chemical derivatization. J Pharm Sci 2014; 103:3033-42. [PMID: 25043726 DOI: 10.1002/jps.24074] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2014] [Revised: 06/01/2014] [Accepted: 06/04/2014] [Indexed: 12/19/2022]
Abstract
The formation of aspartyl succinimide is a common post-translational modification of protein pharmaceuticals under acidic conditions. We present a method to detect and quantitate succinimide in intact protein via hydrazine trapping and chemical derivatization. Succinimide, which is labile under typical analytical conditions, is first trapped with hydrazine to form stable hydrazide and can be directly analyzed by mass spectrometry. The resulting aspartyl hydrazide can be selectively derivatized by various tags, such as fluorescent rhodamine sulfonyl chloride that absorbs strongly in the visible region (570 nm). Our tagging strategy allows the labeled protein to be analyzed by orthogonal methods, including HPLC-UV-Vis, liquid chromatography mass spectrometry (LC-MS), and SDS-PAGE coupled with fluorescence imaging. A unique advantage of our method is that variants containing succinimide, after derivatization, can be readily resolved via either affinity enrichment or chromatographic separation. This allows further investigation of individual factors in a complex protein mixture that affect succinimide formation. Some additional advantages are imparted by fluorescence labeling including the facile detection of the intact protein without proteolytic digestion to peptides; and high sensitivity, for example, without optimization, 0.41% succinimide was readily detected. As such, our method should be useful for rapid screening, optimization of formulation conditions, and related processes relevant to protein pharmaceuticals.
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Affiliation(s)
- Joshua J Klaene
- Barnett Institute of Chemical and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, 02115
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49
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Liu M, Zhang Z, Cheetham J, Ren D, Zhou ZS. Discovery and characterization of a photo-oxidative histidine-histidine cross-link in IgG1 antibody utilizing ¹⁸O-labeling and mass spectrometry. Anal Chem 2014; 86:4940-8. [PMID: 24738698 PMCID: PMC4030806 DOI: 10.1021/ac500334k] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A novel photo-oxidative cross-linking
between two histidines (His-His)
has been discovered and characterized in an IgG1 antibody via the
workflow of XChem-Finder, 18O labeling and mass spectrometry
(Anal. Chem.2013, 85, 5900−590823634697). Its structure was elucidated by peptide
mapping with multiple proteases with various specificities (e.g.,
trypsin, Asp-N, and GluC combined with trypsin or Asp-N) and mass
spectrometry with complementary fragmentation modes (e.g., collision-induced
dissociation (CID) and electron-transfer dissociation (ETD)). Our
data indicated that cross-linking occurred across two identical conserved
histidine residues on two separate heavy chains in the hinge region,
which is highly flexible and solvent accessible. On the basis of model
studies with short peptides, it has been proposed that singlet oxygen
reacts with the histidyl imidazole ring to form an endoperoxide and
then converted to the 2-oxo-histidine (2-oxo-His) and His+32 intermediates, the latter is
subject to a
nucleophilic attack by the unmodified histidine; and finally, elimination
of a water molecule leads to the final adduct with a net mass increase
of 14 Da. Our findings are consistent with this mechanism. Successful
discovery of cross-linked His-His again demonstrates the broad applicability
and utility of our XChem-Finder approach in the discovery and elucidation
of protein cross-linking, particularly without a priori knowledge of the chemical nature and site of cross-linking.
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Affiliation(s)
- Min Liu
- Analytical Research and Development, Amgen , One Amgen Center Drive, Thousand Oaks, California 91320, United States
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50
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Chung MK, Grigoryan H, Iavarone AT, Rappaport SM. Antibody Enrichment and Mass Spectrometry of Albumin-Cys34 Adducts. Chem Res Toxicol 2013; 27:400-7. [DOI: 10.1021/tx400337k] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Ming-Kei Chung
- Center
for Exposure Biology, School of Public Health, University of California, Berkeley, California 94720, United States
| | - Hasmik Grigoryan
- Center
for Exposure Biology, School of Public Health, University of California, Berkeley, California 94720, United States
| | - Anthony T. Iavarone
- Department
of Chemistry and QB3 Institute, University of California, Berkeley, California 94720, United States
| | - Stephen M. Rappaport
- Center
for Exposure Biology, School of Public Health, University of California, Berkeley, California 94720, United States
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