1
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Hsu YP, Nourzaie O, Tocher AE, Nerella K, Ermakov G, Jung J, Fowler A, Wu P, Ayesa U, Willingham A, Beaumont M, Ingale S. Site-Specific Antibody Conjugation Using Modified Bisected N-Glycans: Method Development and Potential toward Tunable Effector Function. Bioconjug Chem 2023; 34:1633-1644. [PMID: 37620302 PMCID: PMC10516122 DOI: 10.1021/acs.bioconjchem.3c00302] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 08/08/2023] [Indexed: 08/26/2023]
Abstract
Antibody-drug conjugates (ADCs) have garnered worldwide attention for disease treatment, as they possess high target specificity, a long half-life, and outstanding potency to kill or modulate the functions of targets. FDA approval of multiple ADCs for cancer therapy has generated a strong desire for novel conjugation strategies with high biocompatibility and controllable bioproperties. Herein, we present a bisecting glycan-bridged conjugation strategy that enables site-specific conjugation without the need for the oligosaccharide synthesis and genetic engineering of antibodies. Application of this method is demonstrated by conjugation of anti-HER2 human and mouse IgGs with a cytotoxic drug, monomethyl auristatin E. The glycan bridge showed outstanding stability, and the resulting ADCs eliminated HER2-expressing cancer cells effectively. Moreover, our strategy preserves the feasibility of glycan structure remodeling to fine-tune the immunogenicity and pharmacokinetic properties of ADCs through glycoengineering.
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Affiliation(s)
- Yen-Pang Hsu
- MRL,
Merck & Co., Inc., 320 Bent St., Cambridge, Massachusetts 02141, United States
| | - Omar Nourzaie
- MRL,
Merck & Co., Inc., 213 E. Grand Ave., South San Francisco, California 94080, United States
| | - Ariel E. Tocher
- MRL,
Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Kavitha Nerella
- MRL,
Merck & Co., Inc., 320 Bent St., Cambridge, Massachusetts 02141, United States
| | - Grigori Ermakov
- MRL,
Merck & Co., Inc., 213 E. Grand Ave., South San Francisco, California 94080, United States
| | - Jiwon Jung
- MRL,
Merck & Co., Inc., 213 E. Grand Ave., South San Francisco, California 94080, United States
| | - Alexandra Fowler
- MRL,
Merck & Co., Inc., 320 Bent St., Cambridge, Massachusetts 02141, United States
| | - Peidong Wu
- MRL,
Merck & Co., Inc., 320 Bent St., Cambridge, Massachusetts 02141, United States
| | - Umme Ayesa
- MRL, Merck
& Co., Inc., 90 E.
Scott Ave., Rahway, New Jersey 07065, United States
| | - Aarron Willingham
- MRL,
Merck & Co., Inc., 213 E. Grand Ave., South San Francisco, California 94080, United States
| | - Maribel Beaumont
- MRL,
Merck & Co., Inc., 213 E. Grand Ave., South San Francisco, California 94080, United States
| | - Sampat Ingale
- MRL,
Merck & Co., Inc., 320 Bent St., Cambridge, Massachusetts 02141, United States
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2
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Metwally E, Mak V, Soriano A, Zebisch M, Silvestre HL, McEwan PA, Ermakov G, Beaumont M, Tawa P, Barker JJ, Yen R, Patel A, Lim YH, Healy D, Hanisak J, Cheng AC, Greshock T, Fischmann TO. Structural insights into selective small molecule activation of PKG1α. Commun Biol 2023; 6:798. [PMID: 37524852 PMCID: PMC10390508 DOI: 10.1038/s42003-023-05095-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 07/04/2023] [Indexed: 08/02/2023] Open
Abstract
cGMP-dependent protein kinase I-α (PKG1α) is a target for pulmonary arterial hypertension due to its role in the regulation of smooth muscle function. While most work has focused on regulation of cGMP turnover, we recently described several small molecule tool compounds which were capable of activating PKG1α via a cGMP independent pathway. Selected molecules were crystallized in the presence of PKG1α and were found to bind to an allosteric site proximal to the low-affinity nucleotide binding domain. These molecules act to displace the switch helix and cause activation of PKG1α representing a new mechanism for the activation and control of this critical therapeutic path. The described structures are vital to understanding the function and control of this key regulatory pathway.
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Affiliation(s)
- Essam Metwally
- Modeling and Informatics, MRL, Merck & Co., Inc., 213 E. Grand Avenue, South San Francisco, CA, USA.
| | - Victor Mak
- Discovery Chemistry, MRL, Merck & Co., Inc., 213 E. Grand Avenue, South San Francisco, CA, USA
| | - Aileen Soriano
- Quantitative Biosciences, MRL, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Matthias Zebisch
- Evotec (UK) Ltd, 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire, OX14 4RZ, UK
| | - H Leonardo Silvestre
- Evotec (UK) Ltd, 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire, OX14 4RZ, UK
| | - Paul A McEwan
- Evotec (UK) Ltd, 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire, OX14 4RZ, UK
| | - Grigori Ermakov
- Discovery Bioanalytics, MRL, Merck & Co., Inc., 213 E. Grand Avenue, South San Francisco, CA, USA
| | - Maribel Beaumont
- Discovery Bioanalytics, MRL, Merck & Co., Inc., 213 E. Grand Avenue, South San Francisco, CA, USA
| | - Paul Tawa
- Quantitative Biosciences, MRL, Merck & Co., Inc., Kenilworth, NJ, USA
| | - John J Barker
- Evotec (UK) Ltd, 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire, OX14 4RZ, UK
| | - Rose Yen
- Discovery Chemistry, MRL, Merck & Co., Inc., 213 E. Grand Avenue, South San Francisco, CA, USA
| | - Akash Patel
- Discovery Chemistry, MRL, Merck & Co., Inc., 213 E. Grand Avenue, South San Francisco, CA, USA
| | - Yeon-Hee Lim
- Discovery Chemistry, MRL, Merck & Co., Inc., 213 E. Grand Avenue, South San Francisco, CA, USA
| | - David Healy
- Discovery Biology, MRL, Merck & Co., Inc., Boston, MA, USA
| | - Jennifer Hanisak
- Discovery Chemistry, MRL, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Alan C Cheng
- Modeling and Informatics, MRL, Merck & Co., Inc., 213 E. Grand Avenue, South San Francisco, CA, USA
| | - Tom Greshock
- Discovery Chemistry, MRL, Merck & Co., Inc., 213 E. Grand Avenue, South San Francisco, CA, USA
| | - Thierry O Fischmann
- Protein and Structural Chemistry, MRL, Merck & Co., Inc., Kenilworth, NJ, USA.
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3
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Dang X, Guelen L, Lutje Hulsik D, Ermakov G, Hsieh EJ, Kreijtz J, Stammen-Vogelzangs J, Lodewijks I, Bertens A, Bramer A, Guadagnoli M, Nazabal A, van Elsas A, Fischmann T, Juan V, Beebe A, Beaumont M, van Eenennaam H. Epitope mapping of monoclonal antibodies: a comprehensive comparison of different technologies. MAbs 2023; 15:2285285. [PMID: 38010385 PMCID: PMC10730160 DOI: 10.1080/19420862.2023.2285285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 11/15/2023] [Indexed: 11/29/2023] Open
Abstract
Monoclonal antibodies have become an important class of therapeutics in the last 30 years. Because the mechanism of action of therapeutic antibodies is intimately linked to their binding epitopes, identification of the epitope of an antibody to the antigen plays a central role during antibody drug development. The gold standard of epitope mapping, X-ray crystallography, requires a high degree of proficiency with no guarantee of success. Here, we evaluated six widely used alternative methods for epitope identification (peptide array, alanine scan, domain exchange, hydrogen-deuterium exchange, chemical cross-linking, and hydroxyl radical footprinting) in five antibody-antigen combinations (pembrolizumab+PD1, nivolumab+PD1, ipilimumab+CTLA4, tremelimumab+CTLA4, and MK-5890+CD27). The advantages and disadvantages of each technique are demonstrated by our data and practical advice on when and how to apply specific epitope mapping techniques during the drug development process is provided. Our results suggest chemical cross-linking most accurately identifies the epitope as defined by crystallography.
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Affiliation(s)
- Xibei Dang
- Pharmacokinetics, Merck & Co. Inc, Kenilworth, NJ, USA
| | - Lars Guelen
- Research, Aduro Biotech Europe, Oss, The Netherlands
| | | | | | | | - Joost Kreijtz
- Research, Aduro Biotech Europe, Oss, The Netherlands
| | | | | | | | - Arne Bramer
- Research, Aduro Biotech Europe, Oss, The Netherlands
| | | | | | | | | | - Veronica Juan
- Pharmacokinetics, Merck & Co. Inc, Kenilworth, NJ, USA
| | - Amy Beebe
- Pharmacokinetics, Merck & Co. Inc, Kenilworth, NJ, USA
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4
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Beaumont M, Tomazela D, Hodges D, Ermakov G, Hsieh E, Figueroa I, So OY, Song Y, Ma H, Antonenko S, Mengesha W, Zhang YW, Zhang S, Hseih S, Ayanoglu G, Du X, Rimmer E, Judo M, Vives F, Yearley JH, Moon C, Manibusan A, Knudsen N, Beck A, Bresson D, Gately D, Neupane D, Escandón E. Antibody-drug conjugates: integrated bioanalytical and biodisposition assessments in lead optimization and selection. AAPS Open 2018. [DOI: 10.1186/s41120-018-0026-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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5
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Sukumar S, Wilson DC, Yu Y, Wong J, Naravula S, Ermakov G, Riener R, Bhagwat B, Necheva AS, Grein J, Churakova T, Mangadu R, Georgiev P, Manfra D, Pinheiro EM, Sriram V, Bailey WJ, Herzyk D, McClanahan TK, Willingham A, Beebe AM, Sadekova S. Characterization of MK-4166, a Clinical Agonistic Antibody That Targets Human GITR and Inhibits the Generation and Suppressive Effects of T Regulatory Cells. Cancer Res 2017; 77:4378-4388. [DOI: 10.1158/0008-5472.can-16-1439] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2016] [Revised: 11/21/2016] [Accepted: 06/06/2017] [Indexed: 11/16/2022]
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6
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Sukumar S, Wison D, Yu Y, Wong J, Naravula S, Ermakov G, Bhagwat B, Grein J, Churakova T, Mangadu R, Sriram V, Bailey W, Herzyk D, Mcclanahan T, Willingham A, Beebe A, Sadekova S. Characterization of MK-4166, a clinical agonistic mAb that targets human GITR and inhibits the generation and activity of Tregs. Eur J Cancer 2016. [DOI: 10.1016/s0959-8049(16)32909-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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7
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Yang X, Wang F, Zhang Y, Wang L, Antonenko S, Zhang S, Zhang YW, Tabrizifard M, Ermakov G, Wiswell D, Beaumont M, Liu L, Richardson D, Shameem M, Ambrogelly A. Comprehensive Analysis of the Therapeutic IgG4 Antibody Pembrolizumab: Hinge Modification Blocks Half Molecule Exchange In Vitro and In Vivo. J Pharm Sci 2015; 104:4002-4014. [DOI: 10.1002/jps.24620] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Revised: 07/15/2015] [Accepted: 08/04/2015] [Indexed: 12/24/2022]
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8
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Orth P, Xiao L, Hernandez LD, Reichert P, Sheth PR, Beaumont M, Yang X, Murgolo N, Ermakov G, DiNunzio E, Racine F, Karczewski J, Secore S, Ingram RN, Mayhood T, Strickland C, Therien AG. Mechanism of action and epitopes of Clostridium difficile toxin B-neutralizing antibody bezlotoxumab revealed by X-ray crystallography. J Biol Chem 2014; 289:18008-21. [PMID: 24821719 DOI: 10.1074/jbc.m114.560748] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The symptoms of Clostridium difficile infections are caused by two exotoxins, TcdA and TcdB, which target host colonocytes by binding to unknown cell surface receptors, at least in part via their combined repetitive oligopeptide (CROP) domains. A combination of the anti-TcdA antibody actoxumab and the anti-TcdB antibody bezlotoxumab is currently under development for the prevention of recurrent C. difficile infections. We demonstrate here through various biophysical approaches that bezlotoxumab binds to specific regions within the N-terminal half of the TcdB CROP domain. Based on this information, we solved the x-ray structure of the N-terminal half of the TcdB CROP domain bound to Fab fragments of bezlotoxumab. The structure reveals that the TcdB CROP domain adopts a β-solenoid fold consisting of long and short repeats and that bezlotoxumab binds to two homologous sites within the CROP domain, partially occluding two of the four putative carbohydrate binding pockets located in TcdB. We also show that bezlotoxumab neutralizes TcdB by blocking binding of TcdB to mammalian cells. Overall, our data are consistent with a model wherein a single molecule of bezlotoxumab neutralizes TcdB by binding via its two Fab regions to two epitopes within the N-terminal half of the TcdB CROP domain, partially blocking the carbohydrate binding pockets of the toxin and preventing toxin binding to host cells.
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Affiliation(s)
- Peter Orth
- From Merck & Co., Inc., Kenilworth, New Jersey 07023
| | - Li Xiao
- From Merck & Co., Inc., Kenilworth, New Jersey 07023
| | | | - Paul Reichert
- From Merck & Co., Inc., Kenilworth, New Jersey 07023
| | - Payal R Sheth
- From Merck & Co., Inc., Kenilworth, New Jersey 07023
| | | | - Xiaoyu Yang
- From Merck & Co., Inc., Kenilworth, New Jersey 07023
| | | | | | | | - Fred Racine
- From Merck & Co., Inc., Kenilworth, New Jersey 07023
| | | | - Susan Secore
- Merck & Co., Inc., West Point, Pennsylvania 19486
| | | | - Todd Mayhood
- From Merck & Co., Inc., Kenilworth, New Jersey 07023
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