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Pires CL, Moreno MJ. Improving the Accuracy of Permeability Data to Gain Predictive Power: Assessing Sources of Variability in Assays Using Cell Monolayers. MEMBRANES 2024; 14:157. [PMID: 39057665 PMCID: PMC11278619 DOI: 10.3390/membranes14070157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Revised: 07/05/2024] [Accepted: 07/11/2024] [Indexed: 07/28/2024]
Abstract
The ability to predict the rate of permeation of new compounds across biological membranes is of high importance for their success as drugs, as it determines their efficacy, pharmacokinetics, and safety profile. In vitro permeability assays using Caco-2 monolayers are commonly employed to assess permeability across the intestinal epithelium, with an extensive number of apparent permeability coefficient (Papp) values available in the literature and a significant fraction collected in databases. The compilation of these Papp values for large datasets allows for the application of artificial intelligence tools for establishing quantitative structure-permeability relationships (QSPRs) to predict the permeability of new compounds from their structural properties. One of the main challenges that hinders the development of accurate predictions is the existence of multiple Papp values for the same compound, mostly caused by differences in the experimental protocols employed. This review addresses the magnitude of the variability within and between laboratories to interpret its impact on QSPR modelling, systematically and quantitatively assessing the most common sources of variability. This review emphasizes the importance of compiling consistent Papp data and suggests strategies that may be used to obtain such data, contributing to the establishment of robust QSPRs with enhanced predictive power.
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Affiliation(s)
- Cristiana L. Pires
- Coimbra Chemistry Center—Institute of Molecular Sciences (CQC-IMS), University of Coimbra, 3004-535 Coimbra, Portugal
- Chemistry Department, Faculty of Science and Technology, University of Coimbra, 3004-535 Coimbra, Portugal
| | - Maria João Moreno
- Coimbra Chemistry Center—Institute of Molecular Sciences (CQC-IMS), University of Coimbra, 3004-535 Coimbra, Portugal
- Chemistry Department, Faculty of Science and Technology, University of Coimbra, 3004-535 Coimbra, Portugal
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Low-temperature librations and dynamical transition in proteins at differing hydration levels. Biomol Concepts 2022; 13:81-88. [DOI: 10.1515/bmc-2022-0007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 02/14/2022] [Indexed: 11/15/2022] Open
Abstract
Abstract
Hydration of water affects the dynamics and in turn the activity of biomacromolecules. We investigated the dependence of the librational oscillations and the dynamical transition on the hydrating conditions of two globular proteins with different structure and size, namely β-lactoglobulin (βLG) and human serum albumin (HSA), by spin-label electron paramagnetic resonance (EPR) in the temperature range of 120–270 K. The proteins were spin-labeled with 5-maleimide spin-label on free cysteins and prepared in the lyophilized state, at low (h = 0.12) and full (h = 2) hydration levels in buffer. The angular amplitudes of librations are small and almost temperature independent for both lyophilized proteins. Therefore, in these samples, the librational dynamics is restricted and the dynamical transition is absent. In the small and compact beta-structured βLG, the angular librational amplitudes increase with temperature and hydrating conditions, whereas hydration-independent librational oscillations whose amplitudes rise with temperature are recorded in the large and flexible alpha-structured HSA. Both βLG and HSA at low and fully hydration levels undergo the dynamical transition at about 230 K. The overall results indicate that protein librational dynamics is activated at the low hydration level h = 0.12 and highlight biophysical properties that are common to other biosamples at cryogenic temperatures.
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Ackermann K, Chapman A, Bode BE. A Comparison of Cysteine-Conjugated Nitroxide Spin Labels for Pulse Dipolar EPR Spectroscopy. Molecules 2021; 26:7534. [PMID: 34946616 PMCID: PMC8706713 DOI: 10.3390/molecules26247534] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/30/2021] [Accepted: 12/03/2021] [Indexed: 11/23/2022] Open
Abstract
The structure-function and materials paradigms drive research on the understanding of structures and structural heterogeneity of molecules and solids from materials science to structural biology. Functional insights into complex architectures are often gained from a suite of complementary physicochemical methods. In the context of biomacromolecular structures, the use of pulse dipolar electron paramagnetic resonance spectroscopy (PDS) has become increasingly popular. The main interest in PDS is providing long-range nanometre distance distributions that allow for identifying macromolecular topologies, validating structural models and conformational transitions as well as docking of quaternary complexes. Most commonly, cysteines are introduced into protein structures by site-directed mutagenesis and modified site-specifically to a spin-labelled side-chain such as a stable nitroxide radical. In this contribution, we investigate labelling by four different commercial labelling agents that react through different sulfur-specific reactions. Further, the distance distributions obtained are between spin-bearing moieties and need to be related to the protein structure via modelling approaches. Here, we compare two different approaches to modelling these distributions for all four side-chains. The results indicate that there are significant differences in the optimum labelling procedure. All four spin-labels show differences in the ease of labelling and purification. Further challenges arise from the different tether lengths and rotamers of spin-labelled side-chains; both influence the modelling and translation into structures. Our comparison indicates that the spin-label with the shortest tether in the spin-labelled side-group, (bis-(2,2,5,5-Tetramethyl-3-imidazoline-1-oxyl-4-yl) disulfide, may be underappreciated and could increase the resolution of structural studies by PDS if labelling conditions are optimised accordingly.
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Affiliation(s)
| | | | - Bela E. Bode
- EaStCHEM School of Chemistry, Biomedical Sciences Research Complex, and Centre of Magnetic Resonance, University of St Andrews, North Haugh, St Andrews KY16 9ST, UK; (K.A.); (A.C.)
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Maleimido-proxyl as an EPR spin label for the evaluation of conformational changes of albumin. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2017; 46:773-787. [DOI: 10.1007/s00249-017-1257-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 08/04/2017] [Accepted: 09/16/2017] [Indexed: 11/25/2022]
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Kristensen K, Urquhart AJ, Thormann E, Andresen TL. Binding of human serum albumin to PEGylated liposomes: insights into binding numbers and dynamics by fluorescence correlation spectroscopy. NANOSCALE 2016; 8:19726-19736. [PMID: 27874129 DOI: 10.1039/c6nr05455b] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Liposomes for medical applications are often administered by intravenous injection. Once in the bloodstream, the liposomes are covered with a "protein corona", which impacts the behavior and eventual fate of the liposomes. Currently, many aspects of the liposomal protein corona are not well understood. For example, there is generally a lack of knowledge about the liposome binding affinities and dynamics of common types of blood plasma proteins. Fluorescence correlation spectroscopy (FCS) is a powerful experimental technique that potentially can provide such knowledge. In this study, we have used FCS to investigate the binding of human serum albumin (HSA) to standard types of PEGylated fluid-phase liposomes (consisting of DOPC and DOPE-PEG2k) and PEGylated gel-phase liposomes (consisting of DSPC and DSPE-PEG2k) with various PEG chain surface densities. We detected no significant binding of HSA to the PEGylated fluid-phase liposomes. In contrast, we found that HSA bound tightly to the PEGylated gel-phase liposomes, although only a low number of HSA molecules could be accommodated per liposome. Overall, we believe that our data provides a useful benchmark for other researchers interested in studying the liposomal protein corona.
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Affiliation(s)
- Kasper Kristensen
- Department of Micro- and Nanotechnology, DTU Nanotech, Technical University of Denmark, 2800 Kongens Lyngby, Denmark. and Center for Nanomedicine and Theranostics, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Andrew J Urquhart
- Department of Micro- and Nanotechnology, DTU Nanotech, Technical University of Denmark, 2800 Kongens Lyngby, Denmark. and Center for Nanomedicine and Theranostics, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Esben Thormann
- Department of Chemistry, DTU Chemistry, Technical University of Denmark, 2800 Kongens Lyngby, Denmark and Center for Nanomedicine and Theranostics, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Thomas L Andresen
- Department of Micro- and Nanotechnology, DTU Nanotech, Technical University of Denmark, 2800 Kongens Lyngby, Denmark. and Center for Nanomedicine and Theranostics, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
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Heterogeneity of protein substates visualized by spin-label EPR. Biophys J 2014; 106:716-22. [PMID: 24507612 DOI: 10.1016/j.bpj.2013.12.039] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Revised: 11/28/2013] [Accepted: 12/19/2013] [Indexed: 11/23/2022] Open
Abstract
The energy landscape of proteins is characterized by a hierarchy of substates, which give rise to conformational heterogeneity at low temperatures. In multiply spin-labeled membranous Na,K-ATPase, this heterogeneous population of conformations is manifest by strong inhomogeneous broadening of the electron paramagnetic resonance (EPR) line shapes and nonexponential spin-echo decays, which undergo a transition to homogeneous broadening and exponential relaxation at higher temperatures (previous study). In this study, we apply these EPR methods to small water-soluble proteins, of the type for which the existence of conformational substates is well established. Both α-helical and β-sheet aqueous proteins that are spin-labeled on a single cysteine residue display spin-echo decays with a single phase-memory time T2M and conventional EPR line shapes with predominantly homogeneous broadening, over a broad range of temperatures from 77 K to ∼ 250 K or higher. Above ∼ 200 K, the residual inhomogeneous broadening is reduced almost to zero. In contrast, both the proteins and the spin label alone, when in a glycerol-water mixture below the glass transition, display heterogeneity in spin-echo phase-memory time and a stronger inhomogeneous broadening of the conventional line shapes, similar to multiply spin-labeled membranous Na,K-ATPase below 200 K. Above 200 K (or the glass transition), a single phase-memory time and predominantly homogeneous broadening are found in both spin-label systems. The results are discussed in terms of solvent-mediated protein transitions, the ability of single spin-label sites to detect conformational heterogeneity, and the desirability of exploring multiple sites for proteins with the size and complexity of the Na,K-ATPase.
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Frahm GE, Cameron BE, Smith JC, Johnston MJW. Generation of fatty acids from 1,2-dipalmitoyl-sn-glycero-3-phosphocholine/cardiolipin liposomes that stabilize recombinant human serum albumin. J Liposome Res 2013; 23:101-9. [PMID: 23294393 DOI: 10.3109/08982104.2012.747535] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
CONTEXT At elevated temperatures, studies have shown that serum albumin undergoes irreversible changes to its secondary structure. Anionic fatty acids and/or anionic surfactants have been shown to stabilize human serum albumin (HSA) against thermal denaturation through bridging hydrophobic domains and cationic amino acids residues of the protein. OBJECTIVE As albumin can readily interact with a variety of liposomes, this study proposes that cardiolipin delivered via 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) liposomes can improve the thermal stability of recombinant HSA produced in Saccharomyces cerevisiae (ScrHSA) in a similar manner to anionic fatty acids. MATERIALS AND METHODS Thermal stability and structure of ScrHSA in the absence and presence of DPPC/cardiolipin liposomes was assessed with U/V circular dichroism spectropolarimetry and protein thermal stability was confirmed with differential scanning calorimetry. RESULTS Although freshly prepared DPPC/cardiolipin liposomes did not improve the stability of ScrHSA, DPPC/cardiolipin liposomes incubated at room temperature for 7 d (7dRT) dramatically improved the thermal stability of the protein. Mass spectrometry analysis identified the presence of fatty acids in the 7dRT liposomes, not identified in freshly prepared liposomes, to which the improved stability was attributed. DISCUSSION AND CONCLUSION The generation of fatty acids is attributed to either the chemical hydrolysis or oxidative cleavage of the unsaturated acyl chains of cardiolipin. By modulating the lipid composition through the introduction of lipids with higher acyl chain unsaturation, it may be possible to generate the stabilizing fatty acids in a more rapid manner.
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Affiliation(s)
- Grant E Frahm
- Centre for Vaccine Evaluation, Biologics and Genetic Therapies Directorate, Health Canada, Ottawa, ON, Canada
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Frahm GE, Cyr TD, Smith DGS, Walrond LD, Johnston MJW. Investigation of the Differences in Thermal Stability of Two Recombinant Human Serum Albumins with 1,2-Dipalmitoyl-sn-glycero-3-phosphocholine Liposomes by UV Circular Dichroism Spectropolarimetry. J Phys Chem B 2012; 116:4661-70. [DOI: 10.1021/jp2125729] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Grant E. Frahm
- Centre for
Vaccine Evaluation, Biologics and Genetic
Therapies Directorate, Health Canada, 251
Sir Frederick Banting Driveway, Ottawa, ON K1A 0K9, Canada
| | - Terry D. Cyr
- Centre for
Vaccine Evaluation, Biologics and Genetic
Therapies Directorate, Health Canada, 251
Sir Frederick Banting Driveway, Ottawa, ON K1A 0K9, Canada
| | - Daryl G. S. Smith
- Centre for
Vaccine Evaluation, Biologics and Genetic
Therapies Directorate, Health Canada, 251
Sir Frederick Banting Driveway, Ottawa, ON K1A 0K9, Canada
| | - Lisa D. Walrond
- Centre for
Vaccine Evaluation, Biologics and Genetic
Therapies Directorate, Health Canada, 251
Sir Frederick Banting Driveway, Ottawa, ON K1A 0K9, Canada
| | - Michael J. W. Johnston
- Centre for
Vaccine Evaluation, Biologics and Genetic
Therapies Directorate, Health Canada, 251
Sir Frederick Banting Driveway, Ottawa, ON K1A 0K9, Canada
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Early stage aggregation of human serum albumin in the presence of metal ions. Int J Biol Macromol 2011; 49:337-42. [DOI: 10.1016/j.ijbiomac.2011.05.011] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2011] [Revised: 05/12/2011] [Accepted: 05/16/2011] [Indexed: 11/19/2022]
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Bahmani B, Gupta S, Upadhyayula S, Vullev VI, Anvari B. Effect of polyethylene glycol coatings on uptake of indocyanine green loaded nanocapsules by human spleen macrophages in vitro. JOURNAL OF BIOMEDICAL OPTICS 2011; 16:051303. [PMID: 21639563 DOI: 10.1117/1.3574761] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Near-infrared (NIR) optically active nanoparticles are promising exogenous chromophores for applications in medical imaging and phototherapy. Since nanoparticles can be rapidly eliminated from the body by cells of the reticuloendothelial system, a thriving strategy to increase their blood circulation time is through surface modification with polyethylene glycol (PEG). We constructed polymeric nanocapsules loaded with indocyanine green (ICG), an FDA-approved NIR dye, and coated with aldehyde-terminated PEG. Using optical absorbance spectroscopy and flow cytometry, we investigated the effect of PEG coating and molecular weight (MW) of PEG [5000 and 30,000 Daltons (Da)] on the phagocytic content of human spleen macrophages incubated with ICG-containing nanocapsules (ICG-NCs) between 15 to 360 min. Our results indicate that surface coating with PEG is an effective method to reduce the phagocytic content of ICG-NCs within macrophages for at least up to 360 min of incubation time. Coating the surface of ICG-NCs with the low MW PEG results in lower phagocytic content of ICG-NCs within macrophages for at least up to 60 min of incubation time as compared to ICG-NCs coated with the high MW PEG. Surface coating of ICG-NCs with PEG is a promising approach to prolong vasculature circulation time of ICG for NIR imaging and phototherapeutic applications.
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Affiliation(s)
- Baharak Bahmani
- Department of Bioengineering, University of California, Riverside, California 92521, USA
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Spontaneous transfer of stearic acids between human serum albumin and PEG:2000-grafted DPPC membranes. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2009; 39:921-7. [DOI: 10.1007/s00249-009-0442-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2009] [Revised: 03/06/2009] [Accepted: 03/09/2009] [Indexed: 10/20/2022]
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