1
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Wood V, Kellerman MA, Groves K, Quaglia M, Topp EM, Matejtschuk P, Dalby PA. Investigation of the Solid-State Interactions in Lyophilized Human G-CSF Using Hydrogen-Deuterium Exchange Mass Spectrometry. Mol Pharm 2024; 21:1965-1976. [PMID: 38516985 PMCID: PMC10988552 DOI: 10.1021/acs.molpharmaceut.3c01211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 03/13/2024] [Accepted: 03/13/2024] [Indexed: 03/23/2024]
Abstract
Hydrogen/deuterium exchange mass spectrometry (HDX-MS) previously elucidated the interactions between excipients and proteins for liquid granulocyte colony stimulating factor (G-CSF) formulations, confirming predictions made using computational structure docking. More recently, solid-state HDX mass spectrometry (ssHDX-MS) was developed for proteins in the lyophilized state. Deuterium uptake in ssHDX-MS has been shown for various proteins, including monoclonal antibodies, to be highly correlated with storage stability, as measured by protein aggregation and chemical degradation. As G-CSF is known to lose activity through aggregation upon lyophilization, we applied the ssHDX-MS method with peptide mapping to four different lyophilized formulations of G-CSF to compare the impact of three excipients on local structure and exchange dynamics. HDX at 22 °C was confirmed to correlate well with the monomer content remaining after lyophilization and storage at -20 °C, with sucrose providing the greatest protection, and then phenylalanine, mannitol, and no excipient leading to progressively less protection. Storage at 45 °C led to little difference in final monomer content among the formulations, and so there was no discernible relationship with total deuterium uptake on ssHDX. Incubation at 45 °C may have led to a structural conformation and/or aggregation mechanism no longer probed by HDX at 22 °C. Such a conformational change was observed previously at 37 °C for liquid-formulated G-CSF using NMR. Peptide mapping revealed that tolerance to lyophilization and -20 °C storage was linked to increased stability in the small helix, loop AB, helix C, and loop CD. LC-MS HDX and NMR had previously linked loop AB and loop CD to the formation of a native-like state (N*) prior to aggregation in liquid formulations, suggesting a similar structural basis for G-CSF aggregation in the liquid and solid states.
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Affiliation(s)
- Victoria
E. Wood
- Department
of Biochemical Engineering, University College
London, London WC1E 6BT, United
Kingdom
| | - Mark-Adam Kellerman
- Department
of Biochemical Engineering, University College
London, London WC1E 6BT, United
Kingdom
| | - Kate Groves
- LGC, Queens Road, Teddington, Middlesex TQ11 0LY, United Kingdom
| | - Milena Quaglia
- LGC, Queens Road, Teddington, Middlesex TQ11 0LY, United Kingdom
| | - Elizabeth M. Topp
- Department
of Industrial and Molecular Pharmaceutics, College of Pharmacy, and
Davidson School of Chemical Engineering, College of Engineering Purdue University, West Lafayette, Indiana 47907, United States
| | - Paul Matejtschuk
- Standardisation
Science, NIBSC, Medicines & Healthcare
Products Regulatory Agency, South Mimms, Hertfordshire EN6 3QG, United
Kingdom
| | - Paul A. Dalby
- Department
of Biochemical Engineering, University College
London, London WC1E 6BT, United
Kingdom
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2
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Kellerman MAW, Almeida T, Rudd TR, Matejtschuk P, Dalby PA. NMR Reveals Functionally Relevant Thermally Induced Structural Changes within the Native Ensemble of G-CSF. Mol Pharm 2022; 19:3242-3255. [PMID: 35948076 PMCID: PMC9449972 DOI: 10.1021/acs.molpharmaceut.2c00398] [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: 12/02/2022]
Abstract
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Structure–function relationships in proteins refer
to a
trade-off between stability and bioactivity, molded by evolution of
the molecule. Identifying which protein amino acid residues jeopardize
global or local stability for the benefit of bioactivity would reveal
residues pivotal to this structure–function trade-off. Here,
we use 15N–1H heteronuclear single quantum
coherence (HSQC) nuclear magnetic resonance (NMR) spectroscopy to
probe the microenvironment and dynamics of residues in granulocyte
colony-stimulating factor (G-CSF) through thermal perturbation. From
this analysis, we identified four residues (G4, A6, T133, and Q134)
that we classed as significant to global stability, given that they
all experienced large environmental and dynamic changes and were closely
correlated to each other in their NMR characteristics. Additionally,
we observe that roughly four structural clusters are subject to localized
conformational changes or partial unfolding prior to global unfolding
at higher temperature. Combining NMR observables with structure relaxation
methods reveals that these structural clusters concentrate around
loop AB (binding site III inclusive). This loop has been previously
implicated in conformational changes that result in an aggregation
prone state of G-CSF. Residues H43, V48, and S63 appear to be pivotal
to an opening motion of loop AB, a change that is possibly also important
for function. Hence, we present here an approach to profiling residues
in order to highlight their potential roles in the two vital characteristics
of proteins: stability and bioactivity.
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Affiliation(s)
- Mark-Adam W Kellerman
- Department of Biochemical Engineering, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Teresa Almeida
- Medicines & Healthcare Products Regulatory Agency, National Institute for Biological Standards and Control (NIBSC), Blanche Lane, South Mimms, Potters Bar, Hertfordshire EN6 3QG, United Kingdom
| | - Timothy R Rudd
- Medicines & Healthcare Products Regulatory Agency, National Institute for Biological Standards and Control (NIBSC), Blanche Lane, South Mimms, Potters Bar, Hertfordshire EN6 3QG, United Kingdom.,Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7BE, United Kingdom
| | - Paul Matejtschuk
- Medicines & Healthcare Products Regulatory Agency, National Institute for Biological Standards and Control (NIBSC), Blanche Lane, South Mimms, Potters Bar, Hertfordshire EN6 3QG, United Kingdom
| | - Paul A Dalby
- Department of Biochemical Engineering, University College London, Gower Street, London WC1E 6BT, United Kingdom
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3
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Zhang C, Mou M, Zhou Y, Zhang W, Lian X, Shi S, Lu M, Sun H, Li F, Wang Y, Zeng Z, Li Z, Zhang B, Qiu Y, Zhu F, Gao J. Biological activities of drug inactive ingredients. Brief Bioinform 2022; 23:6582006. [PMID: 35524477 DOI: 10.1093/bib/bbac160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/01/2022] [Accepted: 04/09/2022] [Indexed: 02/06/2023] Open
Abstract
In a drug formulation (DFM), the major components by mass are not Active Pharmaceutical Ingredient (API) but rather Drug Inactive Ingredients (DIGs). DIGs can reach much higher concentrations than that achieved by API, which raises great concerns about their clinical toxicities. Therefore, the biological activities of DIG on physiologically relevant target are widely demanded by both clinical investigation and pharmaceutical industry. However, such activity data are not available in any existing pharmaceutical knowledge base, and their potentials in predicting the DIG-target interaction have not been evaluated yet. In this study, the comprehensive assessment and analysis on the biological activities of DIGs were therefore conducted. First, the largest number of DIGs and DFMs were systematically curated and confirmed based on all drugs approved by US Food and Drug Administration. Second, comprehensive activities for both DIGs and DFMs were provided for the first time to pharmaceutical community. Third, the biological targets of each DIG and formulation were fully referenced to available databases that described their pharmaceutical/biological characteristics. Finally, a variety of popular artificial intelligence techniques were used to assess the predictive potential of DIGs' activity data, which was the first evaluation on the possibility to predict DIG's activity. As the activities of DIGs are critical for current pharmaceutical studies, this work is expected to have significant implications for the future practice of drug discovery and precision medicine.
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Affiliation(s)
- Chenyang Zhang
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Minjie Mou
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Ying Zhou
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China.,State Key Laboratory for Diagnosis and Treatment of Infectious Disease, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang Provincial Key Laboratory for Drug Clinical Research and Evaluation, The First Affiliated Hospital, Zhejiang University, 79 QingChun Road, Hangzhou, Zhejiang 310000, China
| | - Wei Zhang
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Xichen Lian
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Shuiyang Shi
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Mingkun Lu
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Huaicheng Sun
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Fengcheng Li
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Yunxia Wang
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Zhenyu Zeng
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
| | - Zhaorong Li
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
| | - Bing Zhang
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
| | - Yunqing Qiu
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang Provincial Key Laboratory for Drug Clinical Research and Evaluation, The First Affiliated Hospital, Zhejiang University, 79 QingChun Road, Hangzhou, Zhejiang 310000, China
| | - Feng Zhu
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China.,Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
| | - Jianqing Gao
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China.,Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
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4
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Kyu Ko S, Berner C, Kulakova A, Schneider M, Antes I, Winter G, Harris P, Peters GH. Investigation of the pH-dependent aggregation mechanisms of GCSF using low resolution protein characterization techniques and advanced molecular dynamics simulations. Comput Struct Biotechnol J 2022; 20:1439-1455. [PMID: 35386098 PMCID: PMC8956964 DOI: 10.1016/j.csbj.2022.03.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 03/13/2022] [Accepted: 03/14/2022] [Indexed: 01/19/2023] Open
Abstract
Granulocyte-colony stimulating factor (GCSF) is a widely used therapeutic protein to treat neutropenia. GCSF has an increased propensity to aggregate if the pH is increased above 5.0. Although GCSF is very well experimentally characterized, the exact pH-dependent aggregation mechanism of GCSF is still under debate. This study aimed to model the complex pH-dependent aggregation behavior of GCSF using state-of-the-art simulation techniques. The conformational stability of GCSF was investigated by performing metadynamics simulations, while the protein-protein interactions were investigated using coarse-grained (CG) simulations of multiple GCSF monomers. The CG simulations were directly compared with small-angle X-ray (SAXS) data. The metadynamics simulations demonstrated that the orientations of Trp residues in GCSF are dependent on pH. The conformational change of Trp residues is due to the loss of Trp-His interactions at the physiological pH, which in turn may increase protein flexibility. The helical structure of GCSF was not affected by the pH conditions of the simulations. Our CG simulations indicate that at pH 4.0, the colloidal stability may be more important than the conformational stability of GCSF. The electrostatic potential surface and CG simulations suggested that the basic residues are mainly responsible for colloidal stability as deprotonation of these residues causes a reduction of the highly positively charged electrostatic barrier close to the aggregation-prone long loop regions.
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5
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Wood VE, Groves K, Wong LM, Kong L, Bird C, Wadhwa M, Quaglia M, Matejtschuk P, Dalby PA. Protein Engineering and HDX Identify Structural Regions of G-CSF Critical to Its Stability and Aggregation. Mol Pharm 2021; 19:616-629. [PMID: 34965730 DOI: 10.1021/acs.molpharmaceut.1c00754] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The protein engineering and formulation of therapeutic proteins for prolonged shelf-life remain a major challenge in the biopharmaceutical industry. Understanding the influence of mutations and formulations on the protein structure and dynamics could lead to more predictive approaches to their improvement. Previous intrinsic fluorescence analysis of the chemically denatured granulocyte colony-stimulating factor (G-CSF) suggested that loop AB could subtly reorganize to form an aggregation-prone intermediate state. Hydrogen deuterium exchange mass spectrometry (HDX-MS) has also revealed that excipient binding increased the thermal unfolding transition midpoint (Tm) by stabilizing loop AB. Here, we have combined protein engineering with biophysical analyses and HDX-MS to reveal that increased exchange in a core region of the G-CSF comprising loop AB (ABI, a small helix, ABII) and loop CD packed onto helix B and the beginning of loop BC leads to a decrease in Tm and higher aggregation rates. Furthermore, some mutations can increase the population of the aggregation-prone conformation within the native ensemble, as measured by the greater local exchange within this core region.
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Affiliation(s)
- Victoria E Wood
- Department of Biochemical Engineering, University College London, Gower Street, London WC1E 6BT, U.K
| | - Kate Groves
- National Measurement Laboratory at LGC Ltd, Queens Road, Teddington TW11 0LY, U.K
| | - Lok Man Wong
- Department of Biochemical Engineering, University College London, Gower Street, London WC1E 6BT, U.K
| | - Luyan Kong
- Department of Biochemical Engineering, University College London, Gower Street, London WC1E 6BT, U.K
| | - Christopher Bird
- National Institute for Biological Standards and Control (NIBSC), Blanche Lane, South Mimms, Potters Bar, Hertfordshire EN6 3QG, U.K
| | - Meenu Wadhwa
- National Institute for Biological Standards and Control (NIBSC), Blanche Lane, South Mimms, Potters Bar, Hertfordshire EN6 3QG, U.K
| | - Milena Quaglia
- National Measurement Laboratory at LGC Ltd, Queens Road, Teddington TW11 0LY, U.K
| | - Paul Matejtschuk
- National Institute for Biological Standards and Control (NIBSC), Blanche Lane, South Mimms, Potters Bar, Hertfordshire EN6 3QG, U.K
| | - Paul A Dalby
- Department of Biochemical Engineering, University College London, Gower Street, London WC1E 6BT, U.K
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6
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Chen G, Tao L, Li Z. Recent advancements in mass spectrometry for higher order structure characterization of protein therapeutics. Drug Discov Today 2021; 27:196-206. [PMID: 34571276 DOI: 10.1016/j.drudis.2021.09.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 07/30/2021] [Accepted: 09/20/2021] [Indexed: 01/15/2023]
Abstract
Molecular characterization of higher order structure (HOS) in protein therapeutics is crucial to the selection of candidate molecules, understanding of structure-function relationships, formulation development, stability assessment, and comparability studies. Recent advances in mass spectrometry (MS), including native MS, hydrogen/deuterium exchange (HDX)-MS, and fast photochemical oxidation of proteins (FPOP) coupled with MS, have provided orthogonal ways to characterize HOS of protein therapeutics. In this review, we present the utility of native MS, HDX-MS and FPOP-MS in protein therapeutics discovery and development, with a focus on epitope mapping, aggregation assessment, and comparability studies. We also discuss future trends in the application of these MS methods to HOS characterization.
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Affiliation(s)
- Guodong Chen
- Analytical Development and Attribute Sciences, Biologics Development, Global Product Development and Supply, Bristol Myers Squibb, New Brunswick, NJ, USA.
| | - Li Tao
- Analytical Development and Attribute Sciences, Biologics Development, Global Product Development and Supply, Bristol Myers Squibb, New Brunswick, NJ, USA
| | - Zhengjian Li
- Analytical Development and Attribute Sciences, Biologics Development, Global Product Development and Supply, Bristol Myers Squibb, New Brunswick, NJ, USA
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7
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Rospiccio M, Arsiccio A, Winter G, Pisano R. The Role of Cyclodextrins against Interface-Induced Denaturation in Pharmaceutical Formulations: A Molecular Dynamics Approach. Mol Pharm 2021; 18:2322-2333. [PMID: 33999634 PMCID: PMC8289300 DOI: 10.1021/acs.molpharmaceut.1c00135] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
![]()
Protein-based pharmaceutical
products are subject to a variety
of environmental stressors, during both production and shelf-life.
In order to preserve their structure, and, therefore, functionality,
it is necessary to use excipients as stabilizing agents. Among the
eligible stabilizers, cyclodextrins (CDs) have recently gained interest
in the scientific community thanks to their properties. Here, a computational
approach is proposed to clarify the role of β-cyclodextrin (βCD)
and 2-hydroxypropyl-β-cyclodextrin (HPβCD) against granulocyte
colony-stimulating (GCSF) factor denaturation at the air–water
and ice–water interfaces, and also in bulk water at 300 or
260 K. Both traditional molecular dynamics (MD) simulations and enhanced
sampling techniques (metadynamics, MetaD) are used to shed light on
the underlying molecular mechanisms. Bulk simulations revealed that
CDs were preferentially included within the surface hydration layer
of GCSF, and even included some peptide residues in their hydrophobic
cavity. HPβCD was able to stabilize the protein against surface-induced
denaturation in proximity of the air–water interface, while
βCD had a destabilizing effect. No remarkable conformational
changes of GCSF, or noticeable effect of the CDs, were instead observed
at the ice surface. GCSF seemed less stable at low temperature (260
K), which may be attributed to cold-denaturation effects. In this
case, CDs did not significantly improve conformational stability.
In general, the conformationally altered regions of GCSF seemed not
to depend on the presence of excipients that only modulated the extent
of destabilization with either a positive or a negative effect.
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Affiliation(s)
- Marcello Rospiccio
- Molecular Engineering Laboratory, Department of Applied Science and Technology, Politecnico di Torino, Corso Duca degli Abruzzi 24, Torino 10129, Italy
| | - Andrea Arsiccio
- Molecular Engineering Laboratory, Department of Applied Science and Technology, Politecnico di Torino, Corso Duca degli Abruzzi 24, Torino 10129, Italy
| | - Gerhard Winter
- Department of Pharmacy, Ludwig-Maximilians-University, 81377 Munich, Germany
| | - Roberto Pisano
- Molecular Engineering Laboratory, Department of Applied Science and Technology, Politecnico di Torino, Corso Duca degli Abruzzi 24, Torino 10129, Italy
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