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Caceres-Cortes J, Falk B, Mueller L, Dhar TGM. Perspectives on Nuclear Magnetic Resonance Spectroscopy in Drug Discovery Research. J Med Chem 2024; 67:1701-1733. [PMID: 38290426 DOI: 10.1021/acs.jmedchem.3c02389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
The drug discovery landscape has undergone a significant transformation over the past decade, owing to research endeavors in a wide range of areas leading to strategies for pursuing new drug targets and the emergence of novel drug modalities. NMR spectroscopy has been a technology of fundamental importance to these research pursuits and has seen its use expanded both within and outside of traditional medicinal chemistry applications. In this perspective, we will present advancement of NMR-derived methods that have facilitated the characterization of small molecules and novel drug modalities including macrocyclic peptides, cyclic dinucleotides, and ligands for protein degradation. We will discuss innovations in NMR spectroscopy at the chemistry and biology interface that have broadened NMR's utility from hit identification through lead optimization activities. We will also discuss the promise of emerging NMR approaches in bridging our understanding and addressing challenges in the pursuit of the therapeutic agents of the future.
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Affiliation(s)
- Janet Caceres-Cortes
- Synthesis and Enabling Technologies, Small Molecule Drug Discovery, Bristol-Myers Squibb Company, Princeton, New Jersey 08540, United States
| | - Bradley Falk
- Synthesis and Enabling Technologies, Small Molecule Drug Discovery, Bristol-Myers Squibb Company, Princeton, New Jersey 08540, United States
| | - Luciano Mueller
- Synthesis and Enabling Technologies, Small Molecule Drug Discovery, Bristol-Myers Squibb Company, Princeton, New Jersey 08540, United States
| | - T G Murali Dhar
- Discovery Chemistry, Small Molecule Drug Discovery, Bristol-Myers Squibb Company, Princeton, New Jersey 085401, United States
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2
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Ma J, Pathirana C, Liu DQ, Miller SA. NMR spectroscopy as a characterization tool enabling biologics formulation development. J Pharm Biomed Anal 2023; 223:115110. [DOI: 10.1016/j.jpba.2022.115110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 10/03/2022] [Accepted: 10/11/2022] [Indexed: 11/24/2022]
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Hjalte J, Hossain S, Hugerth A, Sjögren H, Wahlgren M, Larsson P, Lundberg D. Aggregation Behavior of Structurally Similar Therapeutic Peptides Investigated by 1H NMR and All-Atom Molecular Dynamics Simulations. Mol Pharm 2022; 19:904-917. [PMID: 35104408 PMCID: PMC8905580 DOI: 10.1021/acs.molpharmaceut.1c00883] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Understanding of peptide aggregation propensity is an important aspect in pharmaceutical development of peptide drugs. In this work, methodologies based on all-atom molecular dynamics (AA-MD) simulations and 1H NMR (in neat H2O) were evaluated as tools for identification and investigation of peptide aggregation. A series of structurally similar, pharmaceutically relevant peptides with known differences in aggregation behavior (D-Phe6-GnRH, ozarelix, cetrorelix, and degarelix) were investigated. The 1H NMR methodology was used to systematically investigate variations in aggregation with peptide concentration and time. Results show that 1H NMR can be used to detect the presence of coexisting classes of aggregates and the inclusion or exclusion of counterions in peptide aggregates. Interestingly, results suggest that the acetate counterions are included in aggregates of ozarelix and cetrorelix but not in aggregates of degarelix. The peptides investigated in AA-MD simulations (D-Phe6-GnRH, ozarelix, and cetrorelix) showed the same rank order of aggregation propensity as in the NMR experiments. The AA-MD simulations also provided molecular-level insights into aggregation dynamics, aggregation pathways, and the influence of different structural elements on peptide aggregation propensity and intermolecular interactions within the aggregates. Taken together, the findings from this study illustrate that 1H NMR and AA-MD simulations can be useful, complementary tools in early evaluation of aggregation propensity and formulation development for peptide drugs.
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Affiliation(s)
- Johanna Hjalte
- Food Technology, Engineering and Nutrition, Lund University, Box 124, 221 00 Lund, Sweden
| | - Shakhawath Hossain
- Department of Pharmacy, Drug Delivery, Uppsala University, Box 580, 751 23 Uppsala, Sweden
| | - Andreas Hugerth
- Ferring Pharmaceuticals A/S, Amager Strandvej 405, 2770 Kastrup, Denmark
| | - Helen Sjögren
- Ferring Pharmaceuticals A/S, Amager Strandvej 405, 2770 Kastrup, Denmark
| | - Marie Wahlgren
- Food Technology, Engineering and Nutrition, Lund University, Box 124, 221 00 Lund, Sweden
| | - Per Larsson
- Department of Pharmacy, Drug Delivery, Uppsala University, Box 580, 751 23 Uppsala, Sweden
| | - Dan Lundberg
- CR Competence AB, Center for Chemistry and Chemical Engineering, Box 124, 221 00 Lund, Sweden
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Panchal J, Falk BT, Antochshuk V, McCoy MA. Investigating protein-excipient interactions of a multivalent V HH therapeutic protein using NMR spectroscopy. MAbs 2022; 14:2124902. [PMID: 36166705 PMCID: PMC9519013 DOI: 10.1080/19420862.2022.2124902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Multispecific therapeutic proteins come in a variety of formats, including bi- and tri-specific antibodies, dual-variable domain antibodies, and CrossMabs. These multivalent proteins are engineered to interact with multiple therapeutic target proteins with high specificity. Multi-domain proteins can be created by linking together a variety of high-affinity antibody fragments. The choice of protein domains and linkers not only affects the interactions of these molecules with therapeutic targets but also influences the intrinsic behavior in solution that affects their stability. The complexity of solution interactions may translate into developability and manufacturing challenges. Here, we use nuclear magnetic resonance (NMR) spectroscopy to study the solution behavior of a multivalent VHH molecule composed of three flexibly linked heavy-chain-only domains that show dramatic stabilization against thermal degradation in the presence of sucrose. A collection of NMR fingerprinting and profiling methods were used to simultaneously monitor the protein solution behavior and capture details of protein–excipient interactions. We provide a framework to characterize and begin to understand the role of molecular flexibility in protein stabilization with potential applications in the design of novel therapeutic protein scaffolds that include multivalent proteins, fusion proteins, antibody-drug conjugates, and proteins modified with flexible lipids.
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Affiliation(s)
- Jainik Panchal
- Sterile and Specialty Products, Merck & Co Inc, Kenilworth, NJ (United States)
| | - Bradley T Falk
- Mass Spectrometry and Biophysics, Merck & Co Inc, Kenilworth, NJ United States
| | - Valentyn Antochshuk
- Sterile and Specialty Products, Merck & Co Inc, Kenilworth, NJ (United States)
| | - Mark A McCoy
- Mass Spectrometry and Biophysics, Merck & Co Inc, Kenilworth, NJ United States
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Ban D, Rice CT, McCoy MA. Quantification of natural abundance NMR data differentiates the solution behavior of monoclonal antibodies and their fragments. MAbs 2021; 13:1978132. [PMID: 34612804 PMCID: PMC8496538 DOI: 10.1080/19420862.2021.1978132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Biotherapeutics are an important class of molecules for the treatment of a wide range of diseases. They include low molecular weight peptides, highly engineered protein scaffolds and monoclonal antibodies. During their discovery and development, assessments of the biophysical attributes is critical to understanding the solution behavior of therapeutic proteins and for de-risking liabilities. Thus, methods that can quantify, characterize, and provide a basis to inform risks and drive the selection of more optimal antibody and alternative scaffolds are needed. Nuclear Magnetic Resonance (NMR) spectroscopy is a technique that provides a means to probe antibody and antibody-like molecules in solution, at atomic resolution, under any formulated conditions. Here, all samples were profiled at natural abundance requiring no isotope enrichment. We present a numerical approach that quantitates two-dimensional methyl spectra. The approach was tested with a reference dataset that contained different types of antibody and antibody-like molecules. This dataset was processed through a procedure we call a Random Sampling of NMR Peaks for Covariance Analysis. This analysis revealed that the first two components were well correlated with the hydrodynamic radius of the molecules included in the reference set. Higher-order principal components were also linked to dynamic features between different tethered antibody-like molecules and contributed to decisions around candidate selection. The reference set provides a basis to characterize molecules with unknown solution behavior and is sensitive to the behavior of a molecule formulated under different conditions. The approach is independent of protein design, scaffold, formulation and provides a facile method to quantify solution behavior.
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Affiliation(s)
- David Ban
- Department of Computational and Structural Chemistry, Merck & Co., Inc, Kenilworth, NJ, USA
| | - Cory T Rice
- Department of Computational and Structural Chemistry, Merck & Co., Inc, Kenilworth, NJ, USA
| | - Mark A McCoy
- Department of Computational and Structural Chemistry, Merck & Co., Inc, Kenilworth, NJ, USA
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Bramham JE, Podmore A, Davies SA, Golovanov AP. Comprehensive Assessment of Protein and Excipient Stability in Biopharmaceutical Formulations Using 1H NMR Spectroscopy. ACS Pharmacol Transl Sci 2021; 4:288-295. [PMID: 33659867 PMCID: PMC7906489 DOI: 10.1021/acsptsci.0c00188] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Indexed: 01/06/2023]
Abstract
Biopharmaceutical proteins are important drug therapies in the treatment of a range of diseases. Proteins, such as antibodies (Abs) and peptides, are prone to chemical and physical degradation, particularly at the high concentrations currently sought for subcutaneous injections, and so formulation conditions, including buffers and excipients, must be optimized to minimize such instabilities. Therefore, both the protein and small molecule content of biopharmaceutical formulations and their stability are critical to a treatment's success. However, assessing all aspects of protein and small molecule stability currently requires a large number of analytical techniques, most of which involve sample dilution or other manipulations which may themselves distort sample behavior. Here, we demonstrate the application of 1H nuclear magnetic resonance (NMR) spectroscopy to study both protein and small molecule content and stability in situ in high-concentration (100 mg/mL) Ab formulations. We show that protein degradation (aggregation or fragmentation) can be detected as changes in 1D 1H NMR signal intensity, while apparent relaxation rates are specifically sensitive to Ab fragmentation. Simultaneously, relaxation-filtered spectra reveal the presence and degradation of small molecule components such as excipients, as well as changes in general solution properties, such as pH. 1H NMR spectroscopy can thus provide a holistic overview of biopharmaceutical formulation content and stability, providing a preliminary characterization of degradation and acting as a triaging step to guide further analytical techniques.
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Affiliation(s)
- Jack E. Bramham
- Manchester
Institute of Biotechnology and School of Chemistry, Faculty of Science
and Engineering, The University of Manchester, Manchester M1 7DN, U.K.
| | - Adrian Podmore
- Dosage
Form Design & Development, BioPharmaceuticals Development, R&D, AstraZeneca, Cambridge CB21 6GH, U.K.
| | - Stephanie A. Davies
- Dosage
Form Design & Development, BioPharmaceuticals Development, R&D, AstraZeneca, Cambridge CB21 6GH, U.K.
| | - Alexander P. Golovanov
- Manchester
Institute of Biotechnology and School of Chemistry, Faculty of Science
and Engineering, The University of Manchester, Manchester M1 7DN, U.K.
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Joshi S, Khatri LR, Kumar A, Rathore AS. Monitoring size and oligomeric-state distribution of therapeutic mAbs by NMR and DLS: Trastuzumab as a case study. J Pharm Biomed Anal 2020; 195:113841. [PMID: 33371967 DOI: 10.1016/j.jpba.2020.113841] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 12/08/2020] [Accepted: 12/08/2020] [Indexed: 11/17/2022]
Abstract
Monoclonal antibodies (mAbs) are the modalities of choice for immunotherapy. This class of products are known to exhibit considerable heterogeneity with respect to size, aggregation states, and charge. This makes it challenging for biopharmaceutical manufacturers, in particular biosimilar producers, to maintain consistency in product quality. In order to fingerprint these biotherapeutic products, multiple, high-resolution analytical tools are used to characterize the numerous critical quality attributes. Recently, there has been growing interest in enhancing adaptability of 1D and 2D NMR platforms for characterization of higher order structure with emphasis on 1D 1H, 2D 1H-15N and 1H-13C NMR experiments at natural abundance. In this communication, we report the applicability of 2D-DOSY NMR for quantification of colloidal diffusivities, namely diffusion coefficient (and associated hydrodynamic radius) for monomeric IgG1 mAb formulations at physiological conditions. Similarity assessment has been performed for trastuzumab originator (multiple batches) and marketed biosimilars to showcase the applicability of this approach. While dynamic light scattering measurements are known to be sensitive to presence of larger particles with a concentration dependence for estimation of colloidal diffusivities, size estimated by NMR experiments was found to be more in agreement with the computational hydrodynamic size estimations derived from the published crystal structures of intact mAb at formulation concentration.
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Affiliation(s)
- Srishti Joshi
- Department of Chemical Engineering, Indian Institute of Technology, 110016, Hauz Khas, India
| | - Lakshya Raj Khatri
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Ashutosh Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India.
| | - Anurag S Rathore
- Department of Chemical Engineering, Indian Institute of Technology, 110016, Hauz Khas, India.
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