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Janke JJ, Starr CG, Kingsbury JS, Furtmann N, Roberts CJ, Calero-Rubio C. Computational Screening for mAb Colloidal Stability with Coarse-Grained, Molecular-Scale Simulations. J Phys Chem B 2024; 128:1515-1526. [PMID: 38315822 DOI: 10.1021/acs.jpcb.3c05303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
Monoclonal antibodies (mAbs) are an important modality of protein therapeutics with broad applications for numerous diseases. However, colloidal instabilities occurring at high protein concentrations can limit the ability to develop stable, high-concentration liquid dosage forms that are required for patient-centric, device-mediated products. Therefore, it is advantageous to identify colloidally stable mAbs early in the discovery process to ensure that they are selected for development. Experimental screening for colloidal stability can be time- and resource-consuming and is most feasible at the later stages of drug development due to material requirements. Alternatively, computational approaches have emerging potential to provide efficient screening and focus developmental efforts on mAbs with the greatest developability potential, while providing mechanistic relationships for colloidal instability. In this work, coarse-grained, molecular-scale models were fine-tuned to screen for colloidal stability at amino-acid resolution. This model parameterization provides a framework to screen for mAb self-interactions and extrapolate to bulk solution behavior. This approach was applied to a wide array of mAbs under multiple buffer conditions, demonstrating the utility of the presented computational approach to augment early candidate screening and later formulation strategies for protein therapeutics.
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Affiliation(s)
- J Joel Janke
- Biologics Drug Product Development and Manufacturing, Sanofi, Framingham, Massachusetts 01701, United States
| | - Charles G Starr
- Biologics Drug Product Development and Manufacturing, Sanofi, Framingham, Massachusetts 01701, United States
| | - Jonathan S Kingsbury
- Biologics Drug Product Development and Manufacturing, Sanofi, Framingham, Massachusetts 01701, United States
| | - Norbert Furtmann
- Large Molecules Research Platform, Sanofi-Aventis Deutschland GmbH, Frankfurt 65926, Germany
| | - Christopher J Roberts
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Cesar Calero-Rubio
- Biologics Drug Product Development and Manufacturing, Sanofi, Framingham, Massachusetts 01701, United States
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Janke JJ, Yu Y, Pomin VH, Zhao J, Wang C, Linhardt RJ, García AE. Characterization of Heparin's Conformational Ensemble by Molecular Dynamics Simulations and Nuclear Magnetic Resonance Spectroscopy. J Chem Theory Comput 2022; 18:1894-1904. [PMID: 35108013 PMCID: PMC9027489 DOI: 10.1021/acs.jctc.1c00760] [Citation(s) in RCA: 2] [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] [Indexed: 01/09/2023]
Abstract
Heparin is a highly charged, polysulfated polysaccharide and serves as an anticoagulant. Heparin binds to multiple proteins throughout the body, suggesting a large range of potential therapeutic applications. Although its function has been characterized in multiple physiological contexts, heparin's solution conformational dynamics and structure-function relationships are not fully understood. Molecular dynamics (MD) simulations facilitate the analysis of a molecule's underlying conformational ensemble, which then provides important information necessary for understanding structure-function relationships. However, for MD simulations to afford meaningful results, they must both provide adequate sampling and accurately represent the energy properties of a molecule. The aim of this study is to compare heparin's conformational ensemble using two well-developed force fields for carbohydrates, known as GLYCAM06 and CHARMM36, using replica exchange molecular dynamics (REMD) simulations, and to validate these results with NMR experiments. The anticoagulant sequence, an ultra-low-molecular-weight heparin, known as Arixtra (fondaparinux, sodium), was simulated with both parameter sets. The results suggest that GLYCAM06 matches experimental nuclear magnetic resonance three-bond J-coupling values measured for Arixtra better than CHARMM36. In addition, NOESY and ROESY experiments suggest that Arixtra is very flexible in the sub-millisecond time scale and does not adopt a unique structure at 25 C. Moreover, GLYCAM06 affords a much more dynamic conformational ensemble for Arixtra than CHARMM36.
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Affiliation(s)
- J Joel Janke
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Yanlei Yu
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Vitor H Pomin
- Department of BioMolecular Sciences, University of Mississippi, Oxford, Mississippi 38677, United States
| | - Jing Zhao
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Chunyu Wang
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Robert J Linhardt
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Angel E García
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
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Janke JJ, Zhang F, Linhardt RJ, Garcia AE. Heparin-Sclerostin Interactions from Surface Plasmon Resonance and Molecular Dynamics Simulations. Biophys J 2016. [DOI: 10.1016/j.bpj.2015.11.2912] [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: 11/16/2022] Open
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Abstract
Fatty acid aggregation is important for a number of diverse applications: from origins of life research to industrial applications to health and disease. Experiments have characterized the phase behavior of oleic acid mixtures, but the molecular details are complex and hard to probe with many experiments. Coarse-grained molecular dynamics computer simulations and free energy calculations are used to model oleic acid aggregation. From random dispersions, we observe the aggregation of oleic acid monomers into micelles, vesicles, and oil phases, depending on the protonation state of the oleic acid head groups. Worm-like micelles are observed when all the oleic acid molecules are deprotonated and negatively charged. Vesicles form spontaneously if significant amounts of both neutral and negative oleic acid are present. Oil phases form when all the fatty acids are protonated and neutral. This behavior qualitatively matches experimental observations of oleic acid aggregation. To explain the observed phase behavior, we use umbrella sampling free energy calculations to determine the stability of individual monomers in aggregates compared to water. We find that both neutral and negative oleic acid molecules prefer larger aggregates, but neutral monomers prefer negatively charged aggregates and negative monomers prefer neutral aggregates. Both neutral and negative monomers are most stable in a DOPC bilayer, with implications on fatty acid adsorption and cellular membrane evolution. Although the CG model qualitatively reproduces oleic acid phase behavior, we show that an updated polarizable water model is needed to more accurately predict the shift in pKa for oleic acid in model bilayers.
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Affiliation(s)
- J Joel Janke
- Department of Biological Sciences and Centre for Molecular Simulation, University of Calgary , 2500 University Drive, Calgary, AB T2N 1N4, Canada
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Sommer LAM, Janke JJ, Bennett WFD, Bürck J, Ulrich AS, Tieleman DP, Dames SA. Characterization of the Immersion Properties of the Peripheral Membrane Anchor of the FATC Domain of the Kinase “Target of Rapamycin” by NMR, Oriented CD Spectroscopy, and MD Simulations. J Phys Chem B 2014; 118:4817-31. [DOI: 10.1021/jp501533d] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Lisa A. M. Sommer
- Chair
of Biomolecular NMR Spectroscopy, Department of Chemistry, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
| | - J. Joel Janke
- Department
of Biological Sciences and Institute for Biocomplexity and Informatics, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - W. F. Drew Bennett
- Department
of Biological Sciences and Institute for Biocomplexity and Informatics, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Jochen Bürck
- Karlsruhe Institute of Technology (KIT), Institute of Biological Interfaces (IBG-2), P.O.B.
3640, 76021 Karlsruhe, Germany
| | - Anne S. Ulrich
- Karlsruhe Institute of Technology (KIT), Institute of Biological Interfaces (IBG-2), P.O.B.
3640, 76021 Karlsruhe, Germany
| | - D. Peter Tieleman
- Department
of Biological Sciences and Institute for Biocomplexity and Informatics, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Sonja A. Dames
- Chair
of Biomolecular NMR Spectroscopy, Department of Chemistry, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
- Institute
of Structural Biology, Helmholtz Zentrum München, Ingolstädter
Landstrasse 1, 85764 Neuherberg, Germany
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Janke JJ, Drew Bennett W, Tieleman DP. Thermodynamics of Oleic Acid Aggregation from Coarse-Grained Molecular Dynamics Simulations. Biophys J 2013. [DOI: 10.1016/j.bpj.2012.11.955] [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: 10/27/2022] Open
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Porter BF, Ridpath JF, Calise DV, Payne HR, Janke JJ, Baxter DG, Edwards JF. Hypomyelination associated with bovine viral diarrhea virus type 2 infection in a longhorn calf. Vet Pathol 2010; 47:658-63. [PMID: 20448278 DOI: 10.1177/0300985810370014] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
A newborn Longhorn heifer calf presented with generalized tremors, muscle fasciculations, ataxia, and nystagmus. At necropsy, no gross central nervous system lesions were observed. Histologically, the brain and spinal cord had mild to moderate diffuse microgliosis and astrocytosis, minimal nonsuppurative encephalitis, and decreased myelin staining. Ultrastructural examination revealed thinning and absence of myelin sheaths. Various cell types were immunohistochemically positive for bovine viral diarrhea virus (BVDV). Noncytopathogenic BVDV was isolated from the brain and identified as BVDV type 2 by phylogenetic analysis. BVDV-induced hypomyelination is rare and analogous to lesions in neonates infected with border disease and classical swine fever viruses. This is the first documented case of hypomyelination in a calf specifically attributed to BVDV type 2 and the first description of the ultrastructural appearance of BVDV-induced hypomyelination.
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Affiliation(s)
- B F Porter
- Department of Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843-4467, USA.
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Affiliation(s)
- L N Wise
- Texas A&M University Large Animal Clinical Sciences, USA.
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