1
|
Rupreo V, Tissopi R, Baruah K, Roy AS, Bhattacharyya J. Multispectroscopic and Theoretical Investigation on the Binding Interaction of a Neurodegenerative Drug, Lobeline with Human Serum Albumin: Perturbation in Protein Conformation and Hydrophobic-Hydrophilic Surface. Mol Pharm 2024. [PMID: 39037173 DOI: 10.1021/acs.molpharmaceut.4c00651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/23/2024]
Abstract
Lobeline (LOB), a naturally occurring alkaloid, has a broad spectrum of pharmacological activities and therapeutic potential, including applications in central nervous system disorders, drug misuse, multidrug resistance, smoking cessation, depression, and epilepsy. LOB represents a promising compound for developing treatments in various medical fields. However, despite extensive pharmacological profiling, the biophysical interaction between the LOB and proteins remains largely unexplored. In the current article, a range of complementary photophysical and cheminformatics methodologies were applied to study the interaction mechanism between LOB and the carrier protein HSA. Steady-state fluorescence and fluorescence lifetime experiments confirmed the static-quenching mechanisms in the HSA-LOB system. "K" (binding constant) of the HSA-LOB system was determined to be 105 M-1, with a single preferable binding site in HSA. The forces governing the HSA-LOB stable complex were analyzed by thermodynamic parameters and electrostatic contribution. The research also investigated how various metal ions affect complex binding. Site-specific binding studies depict Site I as probable binding in HSA by LOB. We conducted synchronous fluorescence, 3D fluorescence, and circular dichroism studies to explore the structural alteration occurring in the microenvironment of amino acids. To understand the robustness of the HSA-LOB complex, we used theoretical approaches, including molecular docking and MD simulations, and analyzed the principal component analysis and free energy landscape. These comprehensive studies of the structural features of biomolecules in ligand binding are of paramount importance for designing targeted drugs and delivery systems.
Collapse
Affiliation(s)
- Vibeizonuo Rupreo
- Department of Chemistry, National Institute of Technology Nagaland, Chumukedima, Nagaland 797103, India
| | - Rengka Tissopi
- Department of Chemistry, National Institute of Technology Nagaland, Chumukedima, Nagaland 797103, India
| | - Kakali Baruah
- Department of Chemical & Biological Sciences, National Institute of Technology Meghalaya, Shillong 793003, India
| | - Atanu Singha Roy
- Department of Chemical & Biological Sciences, National Institute of Technology Meghalaya, Shillong 793003, India
| | - Jhimli Bhattacharyya
- Department of Chemistry, National Institute of Technology Nagaland, Chumukedima, Nagaland 797103, India
| |
Collapse
|
2
|
Brown SJ, Ryan TM, Drummond CJ, Greaves TL, Han Q. Lysozyme aggregation and unfolding in ionic liquid solvents: Insights from small angle X-ray scattering and high throughput screening. J Colloid Interface Sci 2024; 655:133-144. [PMID: 37931553 DOI: 10.1016/j.jcis.2023.10.139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 10/09/2023] [Accepted: 10/25/2023] [Indexed: 11/08/2023]
Abstract
Understanding protein behaviour is crucial for developing functional solvent systems. Ionic liquids (ILs) are designer salts with versatile ion combinations, where some suppress unfavourable protein behaviour. This work utilizes small angle X-ray scattering (SAXS) to investigate the size and shape changes of model protein hen egg white lysozyme (HEWL) in 137 IL and salt solutions. Guinier, Kratky, and pair distance distribution analysis were used to evaluate the protein size, shape, and aggregation changes in these solvents. At low IL and salt concentration (1 mol%), HEWL remained monodispersed and globular. Most ILs increased HEWL size compared to buffer, while the nitrate and mesylate anions induced the most significant size increases. IL cation branching, hydroxyl groups, and longer alkyl chains counteracted this size increase. Common salts exhibited specific ion effects, while the IL effect varied with concentration due to complex ion-pairing. Protein aggregation and unfolding occurred at 10 mol% IL, altering the protein shape, especially for ILs with multiple alkyl chains on the cation, or with a mesylate/nitrate anion. This study highlights the usefulness of adopting a high-throughput SAXS strategy for understanding IL effects on protein behaviour and provides insights on controlling protein aggregation and unfolding with ILs.
Collapse
Affiliation(s)
- Stuart J Brown
- School of Science, STEM College, RMIT University, Melbourne, VIC 3000, Australia
| | - Timothy M Ryan
- SAXS/WAXS Beamline, Australian Synchrotron, 800 Blackburn Rd, Clayton, VIC 3168, Australia
| | - Calum J Drummond
- School of Science, STEM College, RMIT University, Melbourne, VIC 3000, Australia
| | - Tamar L Greaves
- School of Science, STEM College, RMIT University, Melbourne, VIC 3000, Australia.
| | - Qi Han
- School of Science, STEM College, RMIT University, Melbourne, VIC 3000, Australia.
| |
Collapse
|
3
|
Vlachy V, Kalyuzhnyi YV, Hribar-Lee B, Dill KA. Protein Association in Solution: Statistical Mechanical Modeling. Biomolecules 2023; 13:1703. [PMID: 38136574 PMCID: PMC10742237 DOI: 10.3390/biom13121703] [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: 10/25/2023] [Revised: 11/16/2023] [Accepted: 11/20/2023] [Indexed: 12/24/2023] Open
Abstract
Protein molecules associate in solution, often in clusters beyond pairwise, leading to liquid phase separations and high viscosities. It is often impractical to study these multi-protein systems by atomistic computer simulations, particularly in multi-component solvents. Instead, their forces and states can be studied by liquid state statistical mechanics. However, past such approaches, such as the Derjaguin-Landau-Verwey-Overbeek (DLVO) theory, were limited to modeling proteins as spheres, and contained no microscopic structure-property relations. Recently, this limitation has been partly overcome by bringing the powerful Wertheim theory of associating molecules to bear on protein association equilibria. Here, we review these developments.
Collapse
Affiliation(s)
- Vojko Vlachy
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000 Ljubljana, Slovenia;
| | | | - Barbara Hribar-Lee
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000 Ljubljana, Slovenia;
| | - Ken A. Dill
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, New York, NY 11794, USA;
- Department of Chemistry, Physics and Astronomy, Stony Brook University, New York, NY 11790, USA
| |
Collapse
|
4
|
Vitharana S, Stillahn JM, Katayama DS, Henry CS, Manning MC. Application of Formulation Principles to Stability Issues Encountered During Processing, Manufacturing, and Storage of Drug Substance and Drug Product Protein Therapeutics. J Pharm Sci 2023; 112:2724-2751. [PMID: 37572779 DOI: 10.1016/j.xphs.2023.08.003] [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: 10/14/2022] [Revised: 07/24/2023] [Accepted: 08/07/2023] [Indexed: 08/14/2023]
Abstract
The field of formulation and stabilization of protein therapeutics has become rather extensive. However, most of the focus has been on stabilization of the final drug product. Yet, proteins experience stress and degradation through the manufacturing process, starting with fermentaition. This review describes how formulation principles can be applied to stabilize biopharmaceutical proteins during bioprocessing and manufacturing, considering each unit operation involved in prepration of the drug substance. In addition, the impact of the container on stabilty is discussed as well.
Collapse
Affiliation(s)
| | - Joshua M Stillahn
- Legacy BioDesign LLC, Johnstown, CO 80534, USA; Department of Chemistry, Colorado State University, Fort Collins, CO 80523, USA
| | | | - Charles S Henry
- Department of Chemistry, Colorado State University, Fort Collins, CO 80523, USA
| | - Mark Cornell Manning
- Legacy BioDesign LLC, Johnstown, CO 80534, USA; Department of Chemistry, Colorado State University, Fort Collins, CO 80523, USA.
| |
Collapse
|
5
|
Aliyeva M, Brandão P, Gomes JRB, Coutinho JA, Ferreira O, Pinho SP. Solubilities of Amino Acids in Aqueous Solutions of Chloride or Nitrate Salts of Divalent (Mg 2+ or Ca 2+) Cations. JOURNAL OF CHEMICAL AND ENGINEERING DATA 2022; 67:1565-1572. [PMID: 36568723 PMCID: PMC9777878 DOI: 10.1021/acs.jced.2c00148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
The solubilities of glycine, l-leucine, l-phenylalanine, and l-aspartic acid were measured in aqueous MgCl2, Mg(NO3)2, CaCl2,, and Ca(NO3)2 solutions with concentrations ranging from 0 to 2 mol/kg at 298.2 K. The isothermal analytical method was used combined with the refractive index measurements for composition analysis guaranteeing good accuracy. All salts induced a salting-in effect with a higher magnitude for those containing the Ca2+ cation. The nitrate anions also showed stronger binding with the amino acids, thus increasing their relative solubility more than the chloride anions. In particular, calcium nitrate induces an increase in the amino acid solubility from 2.4 (glycine) to 4.6 fold (l-aspartic acid) compared to the corresponding value in water. Amino acid solubility data in aqueous MgCl2 and CaCl2 solutions collected from the open literature were combined with that from this work, allowing us to analyze the relations between the amino acid structure and the salting-in magnitude.
Collapse
Affiliation(s)
- Mehriban Aliyeva
- Centro
de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal
- CICECO
− Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Paula Brandão
- CICECO
− Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - José R. B. Gomes
- CICECO
− Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - João A.
P. Coutinho
- CICECO
− Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Olga Ferreira
- Centro
de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal
| | - Simão P. Pinho
- Centro
de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal
| |
Collapse
|
6
|
Blanco MA. Computational models for studying physical instabilities in high concentration biotherapeutic formulations. MAbs 2022; 14:2044744. [PMID: 35282775 PMCID: PMC8928847 DOI: 10.1080/19420862.2022.2044744] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Computational prediction of the behavior of concentrated protein solutions is particularly advantageous in early development stages of biotherapeutics when material availability is limited and a large set of formulation conditions needs to be explored. This review provides an overview of the different computational paradigms that have been successfully used in modeling undesirable physical behaviors of protein solutions with a particular emphasis on high-concentration drug formulations. This includes models ranging from all-atom simulations, coarse-grained representations to macro-scale mathematical descriptions used to study physical instability phenomena of protein solutions such as aggregation, elevated viscosity, and phase separation. These models are compared and summarized in the context of the physical processes and their underlying assumptions and limitations. A detailed analysis is also given for identifying protein interaction processes that are explicitly or implicitly considered in the different modeling approaches and particularly their relations to various formulation parameters. Lastly, many of the shortcomings of existing computational models are discussed, providing perspectives and possible directions toward an efficient computational framework for designing effective protein formulations.
Collapse
Affiliation(s)
- Marco A. Blanco
- Materials and Biophysical Characterization, Analytical R & D, Merck & Co., Inc, Kenilworth, NJ USA
| |
Collapse
|
7
|
Džudžević Čančar H, Belak Vivod M, Vlachy V, Lukšič M. Phase stability of aqueous mixtures of bovine serum albumin with low molecular mass salts in presence of polyethylene glycol. J Mol Liq 2022; 349:118477. [PMID: 35082451 PMCID: PMC8786219 DOI: 10.1016/j.molliq.2022.118477] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The stability of bovine serum albumin (BSA) solutions against phase separation caused by cooling the system is studied under the combined influence of added poly(ethylene glycol) (PEG) and alkali halide salts in water as solvent. The phase stability of the system depends on the concentration of the added PEG and its molecular mass, the concentration of the low molecular mass electrolyte and its nature, as also on the pH of the solution. More specifically, the addition of NaCl to the BSA-PEG mixture promotes phase separation at pH = 4.0, where BSA carries the net positive charge in aqueous solution, and it increases the stability of the solution at pH=4.6, i.e., near the isoionic point of the protein. Moreover, at pH = 4.6, the cloud-point temperature decreases in the order from NaF to NaI and from LiCl to CsCl. The order of the salts at pH = 4.0 is exactly reversed: LiCl and NaF show the weakest effect on the cloud-point temperature and the strongest decrease in stability is caused by RbCl and NaNO3. An attempt is made to correlate these observations with the free energies of hydration of the added salt ions and with the effect of adsorption of salt ions on the protein surface on the protein-protein interactions. Kosmotropic salt ions decrease the phase stability of BSA-PEG-salt solutions at pH < pI, while exactly the opposite is true at pH = pI.
Collapse
Affiliation(s)
- Hurija Džudžević Čančar
- University of Sarajevo, Faculty of Pharmacy, Zmaja od Bosne 8, Sarajevo 71000, Bosnia and Herzegovina
| | - Matic Belak Vivod
- Jožef Stefan Institute, Jamova cesta 39, SI-1000 Ljubljana, Slovenia
- University of Ljubljana, Faculty of Chemistry and Chemical Technology, Večna pot 113, SI-1000 Ljubljana, Slovenia
| | - Vojko Vlachy
- University of Ljubljana, Faculty of Chemistry and Chemical Technology, Večna pot 113, SI-1000 Ljubljana, Slovenia
| | - Miha Lukšič
- University of Ljubljana, Faculty of Chemistry and Chemical Technology, Večna pot 113, SI-1000 Ljubljana, Slovenia
| |
Collapse
|
8
|
Ovung A, Jamir N, Bhattacharyya J. Lysozyme binding with sulfa group of antibiotics: comparative binding thermodynamics and computational study. LUMINESCENCE 2022; 37:702-712. [DOI: 10.1002/bio.4211] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 01/21/2022] [Accepted: 02/08/2022] [Indexed: 11/12/2022]
Affiliation(s)
- Aben Ovung
- Department of Chemistry National Institute of Technology Nagaland, Chumukedima Dimapur India
| | - Nungshioba Jamir
- Department of Chemistry National Institute of Technology Nagaland, Chumukedima Dimapur India
| | - Jhimli Bhattacharyya
- Department of Chemistry National Institute of Technology Nagaland, Chumukedima Dimapur India
| |
Collapse
|
9
|
Pusara S, Yamin P, Wenzel W, Krstić M, Kozlowska M. A coarse-grained xDLVO model for colloidal protein-protein interactions. Phys Chem Chem Phys 2021; 23:12780-12794. [PMID: 34048523 DOI: 10.1039/d1cp01573g] [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
Colloidal protein-protein interactions (PPIs) of attractive and repulsive nature modulate the solubility of proteins, their aggregation, precipitation and crystallization. Such interactions are very important for many biotechnological processes, but are complex and hard to control, therefore, difficult to be understood in terms of measurements alone. In diluted protein solutions, PPIs can be estimated from the osmotic second virial coefficient, B22, which has been calculated using different methods and levels of theory. The most popular approach is based on the Derjaguin-Landau-Verwey-Overbeek (DLVO) theory and its extended versions, i.e. xDLVO. Despite much efforts, these models are not fully quantitative and must be fitted to experiments, which limits their predictive value. Here, we report an extended xDLVO-CG model, which extends existing models by a coarse-grained representation of proteins and the inclusion of an additional ion-protein dispersion interaction term. We demonstrate for four proteins, i.e. lysozyme (LYZ), subtilisin (Subs), bovine serum albumin (BSA) and immunoglobulin (IgG1), that semi-quantitative agreement with experimental values without the need to fit to experimental B22 values. While most likely not the final step in the nearly hundred years of research in PPIs, xDLVO-CG is a step towards predictive PPIs calculations that are transferable to different proteins.
Collapse
Affiliation(s)
- Srdjan Pusara
- Institute of Nanotechnology, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.
| | - Peyman Yamin
- Institute of Nanotechnology, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.
| | - Wolfgang Wenzel
- Institute of Nanotechnology, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.
| | - Marjan Krstić
- Institute of Nanotechnology, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany. and Institute of Theoretical Solid State Physics, Karlsruhe Institute of Technology (KIT), Wolfgang-Gaede-Str. 1, 76131 Karlsruhe, Germany
| | - Mariana Kozlowska
- Institute of Nanotechnology, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.
| |
Collapse
|
10
|
Brudar S, Hribar-Lee B. Effect of Buffer on Protein Stability in Aqueous Solutions: A Simple Protein Aggregation Model. J Phys Chem B 2021; 125:2504-2512. [PMID: 33656887 PMCID: PMC8041305 DOI: 10.1021/acs.jpcb.0c10339] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Liquid-liquid phase separation (LLPS) of proteins has recently been associated with the onset of numerous diseases. Despite several studies in this area of protein aggregation, buffer-specific effects always seem to be overlooked. In this study we investigated the influence of buffers on the phase stability of hen egg-white lysozyme (HEWL) and its respective protein-protein interactions by measuring the cloud point temperature, second virial coefficient, and interaction diffusion coefficient of several HEWL-buffer solutions (MOPS, phosphate, HEPES, cacodylate) at pH 7.0. The results indicate that the buffer molecules, depending on their hydration, adsorb on the protein surface, and modulate their electrostatic stability. The obtained information was used to extend the recently developed coarse-grained protein model to incorporate buffer-specific effects. Treated by Wertheim's perturbation theory the model qualitatively correctly predicted the experimentally observed phase separation of all investigated HEWL-buffer solutions, and further allowed us to predict the phase stability of protein formulations even in experimentally unattainable conditions. Since the theory can be straightforwardly extended to include multiple components it presents a useful tool to study protein aggregation in crowded cell-like systems.
Collapse
Affiliation(s)
- Sandi Brudar
- Faculty of Chemistry and Chemical Technology, University of Ljubljana,, Večna pot 113, SI-1000 Ljubljana, Slovenia
| | - Barbara Hribar-Lee
- Faculty of Chemistry and Chemical Technology, University of Ljubljana,, Večna pot 113, SI-1000 Ljubljana, Slovenia
| |
Collapse
|
11
|
Acharyya A, Mukherjee D, Gai F. Assessing the Effect of Hofmeister Anions on the Hydrogen-Bonding Strength of Water via Nitrile Stretching Frequency Shift. J Phys Chem B 2020; 124:11783-11792. [PMID: 33346656 DOI: 10.1021/acs.jpcb.0c06299] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The temperature dependence of the peak frequency (νmax) of the C≡N stretching vibrational spectrum of a hydrogen-bonded C≡N species is known to be a qualitative measure of its hydrogen-bonding strength. Herein, we show that within a two-state framework, this dependence can be analyzed in a more quantitative manner to yield the enthalpy and entropy changes (ΔHHB and ΔSHB) for the corresponding hydrogen-bonding interactions. Using this method, we examine the effect of ten common anions on the strength of the hydrogen-bond(s) formed between water and the C≡N group of an unnatural amino acid, p-cyanophenylalanine (PheCN). We find that based on the ΔHHB values, these anions can be arranged in the following order: HPO42- > OAc- > F- > SO42- ≈ Cl- ≈ (H2O) ≈ ClO4- ≈ NO3- > Br- > SCN- ≈ I-, which differs from the corresponding Hofmeister series. Because PheCN has a relatively small size, the finding that anions having very different charge densities (e.g., SO42- and ClO4-) act similarly suggests that this ranking order is likely the result of specific ion effects. Since proteins contain different backbone and side-chain units, our results highlight the need to assess their individual contributions toward the overall Hofmeister effect in order to achieve a microscopic understanding of how ions affect the physical and chemical properties of such macromolecules. In addition, the analytical method described in the present study is applicable for analyzing the spectral evolution of any vibrational spectra composed of two highly overlapping bands.
Collapse
Affiliation(s)
- Arusha Acharyya
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Debopreeti Mukherjee
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Feng Gai
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| |
Collapse
|
12
|
Srivastava R, Chattopadhyaya M, Bandyopadhyay P. Calculation of salt-dependent free energy of binding of β-lactoglobulin homodimer formation and mechanism of dimer formation using molecular dynamics simulation and three-dimensional reference interaction site model (3D-RISM): diffuse salt ions and non-polar interactions between the monomers favor the dimer formation. Phys Chem Chem Phys 2020; 22:2142-2156. [PMID: 31912070 DOI: 10.1039/c9cp05578a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
There are several important phenomena in chemistry, biology, and physics where molecules (or parts of a molecule) having charges of the same sign come closer together and become stable. DNA condensation, RNA folding, colloid-colloid interactions are some of the examples of this kind. In the current work, we have investigated how β-lactoglobulin, a protein found in milk, in spite of carrying +13 charge, favors the homodimer formation in the presence of salt. We have focussed on calculating the protein-protein binding free energy in the presence of salt and identifying the thermodynamic and microscopic mechanism of the process. Estimation of binding free energy of this salt-dependent process is done by combining molecular dynamics simulation with statistical mechanical theory of three-dimensional reference interaction site model (3D-RISM). Binding free energy is evaluated from the chemical potential of the solutes as opposed to potential of mean force calculation, which gives only a constrained free energy. Our calculated values semi-quantitatively match with the experimental results. By examining the different components of binding free energy, we have found that the role of salt ions (especially of Cl-) is to shift the equilibrium towards the dimer. Non-polar (Lennard-Jones) interactions between the monomers is also favorable to the binding free energy. However, water slightly disfavors the dimer formation. For the microscopic mechanism, heterogeneous of both Na+ and Cl- near the charged residues at the binding interface and change of this charge distribution on dimer formation contribute to the stability. A fine-tuning of enthalpic and entropic effects of salt ions is found to operate at different salt concentrations. Both thermodynamic and microscopic mechanism of dimer formation gives detailed insight into the complex electrostatics of charged protein-protein binding.
Collapse
Affiliation(s)
- Rakesh Srivastava
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India.
| | | | - Pradipta Bandyopadhyay
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India.
| |
Collapse
|
13
|
Metrick MA, do Carmo Ferreira N, Saijo E, Hughson AG, Kraus A, Orrú C, Miller MW, Zanusso G, Ghetti B, Vendruscolo M, Caughey B. Million-fold sensitivity enhancement in proteopathic seed amplification assays for biospecimens by Hofmeister ion comparisons. Proc Natl Acad Sci U S A 2019; 116:23029-23039. [PMID: 31641070 PMCID: PMC6859373 DOI: 10.1073/pnas.1909322116] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Recent work with prion diseases and synucleinopathies indicates that accurate diagnostic methods for protein-folding diseases can be based on the ultrasensitive, amplified measurement of pathological aggregates in biospecimens. A better understanding of the physicochemical factors that control the seeded polymerization of such aggregates, and their amplification in vitro, should allow improvements in existing assay platforms, as well as the development of new assays for other proteopathic aggregates. Here, we systematically investigated the effects of the ionic environment on the polymerization of tau, α-synuclein, and the prion protein (PrP) induced by aggregates in biospecimens. We screened salts of the Hofmeister series, a relative ordering of strongly and weakly hydrated salts that tend to precipitate or solubilize proteins. We found that sensitivities of tau-based assays for Alzheimer's seeds and PrP-based assays for prions were best in weakly hydrated anions. In contrast, we saw an inverse trend with different tau-based assays, improving detection sensitivity for progressive supranuclear palsy seeds by ≈106 Hofmeister analysis also improved detection of sporadic Creutzfeldt-Jakob disease prions in human nasal brushings and chronic wasting disease prions in deer-ear homogenates. Our results demonstrate strong and divergent influences of ionic environments on the amplification and detection of proteopathic seeds as biomarkers for protein-folding diseases.
Collapse
Affiliation(s)
- Michael A Metrick
- Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, NIH, Hamilton, MT 59840
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Natalia do Carmo Ferreira
- Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, NIH, Hamilton, MT 59840
| | - Eri Saijo
- Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, NIH, Hamilton, MT 59840
| | - Andrew G Hughson
- Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, NIH, Hamilton, MT 59840
| | - Allison Kraus
- Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, NIH, Hamilton, MT 59840
| | - Christina Orrú
- Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, NIH, Hamilton, MT 59840
| | - Michael W Miller
- Colorado Division of Parks and Wildlife, Wildlife Health Program, Fort Collins, CO 80521-1049
| | - Gianluigi Zanusso
- Department of Neurosciences, University of Verona, 37129 Verona, Italy
| | - Bernardino Ghetti
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN 46202
| | - Michele Vendruscolo
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Byron Caughey
- Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, NIH, Hamilton, MT 59840;
| |
Collapse
|
14
|
Wang W, Ohtake S. Science and art of protein formulation development. Int J Pharm 2019; 568:118505. [PMID: 31306712 DOI: 10.1016/j.ijpharm.2019.118505] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Revised: 07/08/2019] [Accepted: 07/08/2019] [Indexed: 02/07/2023]
Abstract
Protein pharmaceuticals have become a significant class of marketed drug products and are expected to grow steadily over the next decade. Development of a commercial protein product is, however, a rather complex process. A critical step in this process is formulation development, enabling the final product configuration. A number of challenges still exist in the formulation development process. This review is intended to discuss these challenges, to illustrate the basic formulation development processes, and to compare the options and strategies in practical formulation development.
Collapse
Affiliation(s)
- Wei Wang
- Biological Development, Bayer USA, LLC, 800 Dwight Way, Berkeley, CA 94710, United States.
| | - Satoshi Ohtake
- Pharmaceutical Research and Development, Pfizer Biotherapeutics Pharmaceutical Sciences, Chesterfield, MO 63017, United States
| |
Collapse
|
15
|
Dahal YR, Schmit JD. Ion Specificity and Nonmonotonic Protein Solubility from Salt Entropy. Biophys J 2019; 114:76-87. [PMID: 29320698 DOI: 10.1016/j.bpj.2017.10.040] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 10/16/2017] [Accepted: 10/26/2017] [Indexed: 10/18/2022] Open
Abstract
The addition of salt to protein solutions can either increase or decrease the protein solubility, and the magnitude of this effect depends on the salt used. We show that these effects can be captured using a theory that includes attractive and repulsive electrostatic interactions, nonelectrostatic protein-ion interactions, and ion-solvent interactions via an effective solvated ion radius. We find that the ion radius has significant effects on the translational entropy of the salt, which leads to salt specificity in the protein solubility. At low salt, the dominant effect comes from the entropic cost of confining ions within the aggregate, whereas at high concentrations, the salt drives a depletion attraction that favors aggregation. Our theory explains the reversal in the Hofmeister series observed in lysozyme cloud point measurements and semi-quantitatively describes the solubility of lysozyme and chymosin crystals. We present a comparison of the contributions to the free energy and give guidelines for when salting in or salting out should be expected.
Collapse
Affiliation(s)
- Yuba Raj Dahal
- Department of Physics, Kansas State University, Manhattan, Kansas
| | - Jeremy D Schmit
- Department of Physics, Kansas State University, Manhattan, Kansas.
| |
Collapse
|
16
|
Kalyuzhnyi YV, Vlachy V. Modeling the depletion effect caused by an addition of polymer to monoclonal antibody solutions. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2018; 30:485101. [PMID: 30418950 PMCID: PMC6693579 DOI: 10.1088/1361-648x/aae914] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
We present a theoretical study of colloidal stability of the model mixtures of monoclonal antibody molecules and non-adsorbing (no polymer-protein attraction) polymers. The antibodies are pictured as an assembly of seven hard spheres assuming a Y-like shape. Polymers present in the mixture are modeled as chain-like molecules having from 32 up to 128 monomers represented as hard spheres. We use Wertheim's thermodynamic perturbation theory to construct the two molecular species and to calculate measurable properties. The calculations are performed in the osmotic ensemble. In view that no direct attractive interaction is present in the model Hamiltonian, we only account for the entropic contribution to the phase equilibrium. We calculate chemical potentials and the equation of state for the model mixture to determine the liquid-liquid part of the phase diagram. We investigate how the critical antibody number density depends on the degree of polymerization and the bead size ratio of the polymer and protein components. The model mixture qualitatively correctly predicts some basic features of real systems. The effects of the model 'protein' geometry, that is the difference in results for the flexible Y-shaped protein versus the rigid spherical one, are also examined.
Collapse
Affiliation(s)
- Yu V Kalyuzhnyi
- Department of Chemistry, Faculty of Science, J E Purkinje University, 400 96 Ústí nad Labem, Czechia
| | | |
Collapse
|
17
|
Janc T, Vlachy V, Lukšič M. Calorimetric studies of interactions between low molecular weight salts and bovine serum albumin in water at pH values below and above the isoionic point. J Mol Liq 2018; 270:74-80. [PMID: 30872874 DOI: 10.1016/j.molliq.2017.10.105] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Isothermal titration calorimetry was used to determine the temperature and salt concentration dependence of the enthalpy of mixing, Δmix H, of bovine serum albumin (BSA) in aqueous buffer solutions with several low molecular weight salts. Three buffers were used: acetate (pH = 4.0), MOPS (7.2), and borate (9.2). Since the isoionic point of BSA is at pI ≈ 4.7, the net charge of BSA in acetate buffer was positive (≈ +20), while in the other two buffer solutions it was negative (≈ -15 in MOPS and ≈ -25 in borate). The majority of the recorded heat effects were exothermic, while only at pH = 9.2 a weak endothermic effect upon mixing BSA with LiCl, NaCl, and KCl was observed. For all buffer solutions the absolute values of Δmix H of sodium salts followed the order: NaCl < NaBr < NaNO3 < NaI < NaSCN, which is the reverse Hofmeister series for anions. The magnitude of the effects was the largest in acetate buffer and decreased with an increasing pH value of the solution. While the effect of varying the anion of the added salts was strongly pronounced at all pH values, the effect of the cation (LiCl, NaCl, KCl, RbCl and CsCl salts) was weak. The most interesting feature of the results obtained for pH > pI was the fact that Δmix H were considerably more sensitive to the anion (co-ion to the net BSA charge) than to the cation species. This indicated that anions interacted quite strongly with the BSA even at pH values where the net charge of the protein was negative. We showed that Δmix H at high addition of salts correlated well with the enthalpy of hydration of the corresponding salt anion. This finding suggested, consistently with some previous studies, that a part of the exothermic contribution to Δmix H originated from the hydration changes upon the protein-salt interaction. Theoretical analysis, based on the primitive model of highly asymmetric electrolyte solutions solved within the mean spherical approximation, was used to estimate Coulomb effects upon mixing.
Collapse
Affiliation(s)
- Tadeja Janc
- University of Ljubljana, Faculty of Chemistry and Chemical Technology, Večna pot 113, SI-1000 Ljubljana, Slovenia
| | - Vojko Vlachy
- University of Ljubljana, Faculty of Chemistry and Chemical Technology, Večna pot 113, SI-1000 Ljubljana, Slovenia
| | - Miha Lukšič
- University of Ljubljana, Faculty of Chemistry and Chemical Technology, Večna pot 113, SI-1000 Ljubljana, Slovenia
| |
Collapse
|
18
|
Kastelic M, Dill KA, Kalyuzhnyi YV, Vlachy V. Controlling the viscosities of antibody solutions through control of their binding sites. J Mol Liq 2018; 270:234-242. [PMID: 30906093 PMCID: PMC6425977 DOI: 10.1016/j.molliq.2017.11.106] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
For biotechnological drugs, it is desirable to formulate antibody solutions with low viscosities. We go beyond previous colloid theories in treating protein-protein self-association of molecules that are antibody-shaped and flexible and have spatially specific binding sites. We consider interactions either through fragment antigen (Fab-Fab) or fragment crystalizable (Fab-Fc) binding. Wertheim's theory is adapted to compute the cluster-size distributions, viscosities, second virial coefficients, and Huggins coefficients, as functions of antibody concentration. We find that the aggregation properties of concentrated solutions can be anticipated from simpler-to-measure dilute solutions. A principal finding is that aggregation is controllable, in principle, through modifying the antibody itself, and not just the solution it is dissolved in. In particular: (i) monospecific antibodies having two identical Fab arms can form linear chains with intermediate viscosities. (ii) Bispecific antibodies having different Fab arms can, in some cases, only dimerize, having low viscosities. (iii) Arm-to-Fc binding allows for three binding partners, leading to networks and high viscosities.
Collapse
Affiliation(s)
- Miha Kastelic
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, SI-1000 Ljubljana, Slovenia
| | - Ken A. Dill
- Laufer Center for Physical and Quantitative Biology and Departments of Physics and Chemistry, Stony Brook University, Stony Brook, NY 11794
| | - Yura V. Kalyuzhnyi
- Institute for Condensed Matter Physics, Svientsitskii 1, 79011 Lviv, Ukraine
| | - Vojko Vlachy
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, SI-1000 Ljubljana, Slovenia
| |
Collapse
|
19
|
Kastelic M, Vlachy V. Theory for the Liquid-Liquid Phase Separation in Aqueous Antibody Solutions. J Phys Chem B 2018; 122:5400-5408. [PMID: 29338267 PMCID: PMC5980754 DOI: 10.1021/acs.jpcb.7b11458] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
This study presents the theory for liquid-liquid phase separation for systems of molecules modeling monoclonal antibodies. Individual molecule is depicted as an assembly of seven hard spheres, organized to mimic the Y-shaped antibody. We consider the antibody-antibody interactions either through Fab, Fab' (two Fab fragments may be different), or Fc domain. Interaction between these three domains of the molecule (hereafter denoted as A, B, and C, respectively) is modeled by a short-range square-well attraction. To obtain numerical results for the model under study, we adapt Wertheim's thermodynamic perturbation theory. We use this model to calculate the liquid-liquid phase separation curve and the second virial coefficient B2. Various interaction scenarios are examined to see how the strength of the site-site interactions and their range shape the coexistence curve. In the asymmetric case, where an attraction between two sites is favored and the interaction energies for the other sites kept constant, critical temperature first increases and than strongly decreases. Some more microscopic information, for example, the probability for the particular two sites to be connected, has been calculated. Analysis of the experimental liquid-liquid phase diagrams, obtained from literature, is presented. In addition, we calculate the second virial coefficient under conditions leading to the liquid-liquid phase separation and present this quantity on the graph B2 versus protein concentration.
Collapse
Affiliation(s)
| | - Vojko Vlachy
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, SI-1000 Ljubljana, Slovenia
| |
Collapse
|
20
|
The scientific life of Vojko Vlachy. J Mol Liq 2017. [DOI: 10.1016/j.molliq.2016.11.073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|