Mutational and biophysical robustness in a prestabilized monobody.

The fibronectin type III (FN3) monobody domain is a promising non-antibody scaffold, which features a less complex architecture than an antibody while maintaining analogous binding loops. We previously developed FN3Con, a hyperstable monobody derivative with diagnostic and therapeutic potential. Prestabilization of the scaffold mitigates the stability-function trade-off commonly associated with evolving a protein domain toward biological activity. Here, we aimed to examine if the FN3Con monobody could take on antibody-like binding to therapeutic targets, while retaining its extreme stability. We targeted the first of the Adnectin derivative of monobodies to reach clinical trials, which was engineered by directed evolution for binding to the therapeutic target VEGFR2; however, this function was gained at the expense of large losses in thermostability and increased oligomerization. In order to mitigate these losses, we grafted the binding loops from Adnectin-anti-VEGFR2 (CT-322) onto the prestabilized FN3Con scaffold to produce a domain that successfully bound with high affinity to the therapeutic target VEGFR2. This FN3Con-anti-VEGFR2 construct also maintains high thermostability, including remarkable long-term stability, retaining binding activity after 2 years of storage at 36 °C. Further investigations into buffer excipients doubled the presence of monomeric monobody in accelerated stability trials. These data suggest that loop grafting onto a prestabilized scaffold is a viable strategy for the development of monobody domains with desirable biophysical characteristics and that FN3Con is therefore well-suited to applications such as the evolution of multiple paratopes or shelf-stable diagnostics and therapeutics.

Design and in-vitro testing of a portable patient isolation chamber for bedside aerosol containment and filtration.

The emergence of the SARS-CoV-2 pandemic has imposed a multitude of complications on healthcare facilities. Healthcare professionals had to develop creative solutions to deal with resource shortages and isolation spaces when caring for COVID positive patients. Among many other solutions, facilities have utilized engineering strategies to mitigate the spread of viral contamination within the hospital environment. One of the standard solutions has been the use of whole room negative pressurization (WRNP) to turn a general patient room into an infection isolation space. However, this has not always been easy due to many limitations, such as direct access to the outdoors and the availability of WRNP units. In operating rooms where a patient is likely to go through aerosol-generating procedures, other solutions must be considered because most operating rooms use positive pressure ventilation to maintain sterility. The research team has designed, built, and tested a Covering for Operations during Viral Emergency Response (COVER), a low-cost, portable isolation chamber that fits over a patient's torso on a hospital bed to contain and remove the pathogenic agents at the source (i.e., patient's mouth and nose). This study tests the performance of the COVER system under various design and performance scenarios using particle tracing techniques and compares its efficiency with WRNP units. The results show that COVER can dramatically reduce the concentration of particles within the room, while WRNP is only effective in preventing the room-induced particles from migrating to adjacent spaces.

Applications of isothermal titration calorimetry in pure and applied research from 2016 to 2020.

The last 5 years have seen a series of advances in the application of isothermal titration microcalorimetry (ITC) and interpretation of ITC data. ITC has played an invaluable role in understanding multiprotein complex formation including proteolysis-targeting chimeras (PROTACS), and mitochondrial autophagy receptor Nix interaction with LC3 and GABARAP. It has also helped elucidate complex allosteric communication in protein complexes like trp RNA-binding attenuation protein (TRAP) complex. Advances in kinetics analysis have enabled the calculation of kinetic rate constants from pre-existing ITC data sets. Diverse strategies have also been developed to study enzyme kinetics and enzyme-inhibitor interactions. ITC has also been applied to study small molecule solvent and solute interactions involved in extraction, separation, and purification applications including liquid-liquid separation and extractive distillation. Diverse applications of ITC have been developed from the analysis of protein instability at different temperatures, determination of enzyme kinetics in suspensions of living cells to the adsorption of uremic toxins from aqueous streams.

Phytase catalysis of dephosphorylation studied using isothermal titration calorimetry and electrospray ionization time-of-flight mass spectroscopy.

Phytases are important commercial enzymes that catalyze the dephosphorylation of myo-inositol hexakisphosphate (phytate) to its lower inositol phosphate (IP) esters, IP6 to IP1. Digestion of phytate by Citrobacter braakii 6-phytase deviates significantly from monophasic Michaelis-Menten kinetics. Analysis of phytate digestion using isothermal titration calorimetry (ITC) using the single injection method produced a thermogram with two peaks consistent with two periods of high enzyme activity. Continuous-flow electrospray ionization time-of-flight mass spectroscopy (ESI-ToF-MS) provided real-time analysis of phytase catalysis. It was able to show that the first two cleavage steps were rapid and concurrent but the third cleavage step from IP4 to IP3 was slow. The third (IP4 to IP3), fourth (IP3 to IP2) and fifth (IP2 to IP1) cleavages were effectively sequential due to the preferred association of the more phosphorylated species with the phytase catalytic site. This created a bottleneck during the cleavage of IP4 to IP3 until the point at which IP4 was exhausted and was followed by the rapid cleavage of IP3 to IP2, which was observed as the second peak in the ITC thermogram. This work illustrates the importance of an orthogonal approach when studying non-specific or complex enzyme catalyzed reactions.

Applications of isothermal titration calorimetry - the research and technical developments from 2011 to 2015.

Isothermal titration calorimetry is a widely used biophysical technique for studying the formation or dissociation of molecular complexes. Over the last 5 years, much work has been published on the interpretation of isothermal titration calorimetry (ITC) data for single binding and multiple binding sites. As over 80% of ITC papers are on macromolecules of biological origin, this interpretation is challenging. Some researchers have attempted to link the thermodynamics constants to events at the molecular level. This review highlights work carried out using binding sites characterized using x-ray crystallography techniques that allow speculation about individual bond formation and the displacement of individual water molecules during ligand binding and link these events to the thermodynamic constants for binding. The review also considers research conducted with synthetic binding partners where specific binding events like anion-π and π-π interactions were studied. The revival of assays that enable both thermodynamic and kinetic information to be collected from ITC data is highlighted. Lastly, published criticism of ITC research from a physical chemistry perspective is appraised and practical advice provided for researchers unfamiliar with thermodynamics and its interpretation. Copyright © 2016 John Wiley & Sons, Ltd.

A study of the relationship between water and anions of the Hofmeister series using pressure perturbation calorimetry.

Pressure perturbation calorimetry (PPC) was used to study the relationship between water and sodium salts with a range of different anions. At temperatures around 25 °C the heat on pressurisation (ΔQ) from 1 to 5 bar was negative for all solutions relative to pure water. The raw data showed that as the temperature rose, the gradient was positive relative to pure water and the transition temperature where ΔQ was zero was related to anion surface charge density and was more pronounced for the low-charge density anions. A three component model was developed comprising bulk water, the hydration layer and the solute to calculate the molar expansivity of the hydration layer around the ions in solution. The calculated molar expansivities of water in the hydration layer around the ions were consistently less than pure water. ΔQ at different disodium hydrogen phosphate concentrations showed that the change in molar enthalpy relative to pure water was not linear even as it approached infinite dilution suggesting that while hydration layers can be allocated to the water around ions this does not rule out interactions between water and ions extending beyond the immediate hydration layer.

Analysis of the hydration water around bovine serum albumin using terahertz coherent synchrotron radiation.

Terahertz spectroscopy was used to study the absorption of bovine serum albumin (BSA) in water. The Diamond Light Source operating in a low alpha mode generated coherent synchrotron radiation that covered a useable spectral bandwidth of 0.3-3.3 THz (10-110 cm(-1)). As the BSA concentration was raised, there was a nonlinear change in absorption inconsistent with Beer's law. At low BSA concentrations (0-1 mM), the absorption remained constant or rose slightly. Above a concentration of 1 mM BSA, a steady decrease in absorption was observed, which was followed by a plateau that started at 2.5 mM. Using a overlapping hydration layer model, the hydration layer was estimated to extend 15 Å from the protein. Calculation of the corrected absorption coefficient (αcorr) for the water around BSA by subtracting the excluded volume of the protein provides an alternative approach to studying the hydration layer that provides evidence for complexity in the population of water around BSA.

Biopharmaceutical liquid formulation: a review of the science of protein stability and solubility in aqueous environments.

Formulation scientists employed in the biopharmaceutical industry face the challenge of creating liquid aqueous formulations for proteins that never had evolutionary pressure to be exceptionally stable or soluble. Yet commercial products usually need a shelf life of 2 years to be economically viable. The research done in this field is dominated by physical chemists who have developed theories like preferential interaction, preferential hydration and excluded volume to explain the mechanisms for the interaction between salt, small organic molecules and proteins. This review aims to translate the research findings on protein stability and solubility produced by the physical chemists and make it accessible to formulation scientists working within the biopharmaceutical industry.

Applications of isothermal titration calorimetry in pure and applied research--survey of the literature from 2010.

Isothermal titration calorimetry (ITC) is a biophysical technique for measuring the formation and dissociation of molecular complexes and has become an invaluable tool in many branches of science from cell biology to food chemistry. By measuring the heat absorbed or released during bond formation, ITC provides accurate, rapid, and label-free measurement of the thermodynamics of molecular interactions. In this review, we survey the recent literature reporting the use of ITC and have highlighted a number of interesting studies that provide a flavour of the diverse systems to which ITC can be applied. These include measurements of protein-protein and protein-membrane interactions required for macromolecular assembly, analysis of enzyme kinetics, experimental validation of molecular dynamics simulations, and even in manufacturing applications such as food science. Some highlights include studies of the biological complex formed by Staphylococcus aureus enterotoxin C3 and the murine T-cell receptor, the mechanism of membrane association of the Parkinson's disease-associated protein α-synuclein, and the role of non-specific tannin-protein interactions in the quality of different beverages. Recent developments in automation are overcoming limitations on throughput imposed by previous manual procedures and promise to greatly extend usefulness of ITC in the future. We also attempt to impart some practical advice for getting the most out of ITC data for those researchers less familiar with the method.

Development and efficacy testing of a portable negative pressure enclosure for airborne infection containment.

OBJECTIVES: To overcome the shortage of personal protective equipment and airborne infection isolation rooms (AIIRs) in the COVID-19 pandemic, a collaborative team of research engineers and clinical physicians worked to build a novel negative pressure environment in the hopes of improving healthcare worker and patient safety. The team then sought to test the device's efficacy in generating and maintaining negative pressure. The goal proved prescient as the US Food and Drug Administration (FDA) later recommended that all barrier devices use negative pressure. METHODS: Initially, engineers observed simulations of various aerosol- and droplet-generating procedures using hospital beds and stretchers to determine the optimal working dimensions of the containment device. Several prototypes were made based on these dimensions which were combined with filters and various flow-generating devices. Then, the airflow generated and the pressure differential within the device during simulated patient care were measured, specifically assessing its ability to create a negative pressure environment consistent with standards published by the Centers for Disease Control and Prevention (CDC). RESULTS: The portable fans were unable to generate any airflow and were dropped from further testing. The vacuums tested were all able to generate a negative pressure environment with the magnitude of pressure differential increasing with the vacuum horsepower. Only the 3.5-horsepower Shop-Vac, however, generated a -3.0 pascal (Pa) pressure gradient, exceeding the CDC-recommended minimum of -2.5 Pa for AIIRs. CONCLUSION: A collaborative team of physicians and engineers demonstrated the efficacy of a prototype portable negative pressure environment, surpassing the negative pressure differential recommended by the CDC.

Survey of the year 2009: applications of isothermal titration calorimetry.

Isothermal titration calorimetry (ITC) is now an established and invaluable method for determining the thermodynamic constants, association constant and stoichiometry of molecular interactions in aqueous solutions. The technique has become widely used by biochemists to study protein interaction with other proteins, small molecules, metal ions, lipids, nucleic acids and carbohydrates; and nucleic acid interaction with small molecules. The drug discovery industry has utilized this approach to measure protein (or nucleic acid) interaction with drug candidates. ITC has been used to screen candidates, guide the design of potential drugs and validate the modelling used in structure-based drug design. Emerging disciplines including nanotechnology and drug delivery could benefit greatly from ITC in enhancing their understanding and control of nano-particle assembly, and drug binding and controlled release.

Characterization of low-frequency modes in aqueous peptides using far-infrared spectroscopy and molecular dynamics simulation.

Far-infrared spectroscopy was used to study the dynamics of three aqueous peptides having varied helicity. Experimental data were compared to the molecular dynamics simulated far-infrared absorbance spectrum derived from the dipole time correlation function. Vibrational density of state (VDOS) simulation was then used to analyze the contribution of different structural elements to the bands. Frozen aqueous peptide samples were studied in the frequency range between 325 and 540 cm(-1) where the ice absorbance is low. Three resonances were identified; band I centered at approximately 333 cm(-1), band II centered at approximately 380 cm(-1), and band III comprising two constituent bands at approximately 519 and 528 cm(-1). The peak height and frequency of the maximum absorbance of bands I and II varied depending on the helicity of the peptide. VDOS of the far-infrared absorbance spectrum confirmed that bands I and II were associated with the peptide backbone and that band III had both potential backbone and side chain components.

Latent Anti-nutrients and Unintentional Breeding Consequences in Australian Sorghum bicolor Varieties.

Modern feed quality sorghum grain has been bred to reduce anti-nutrients, most conspicuously condensed tannins, but its inclusion in the diets of monogastric animals can still result in variable performance that is only partially understood. Sorghum grain contains several negative intrinsic factors, including non-tannin phenolics and polyphenols, phytate, and kafirin protein, which may be responsible for these muted feed performances. To better understand the non-tannin phenolic and polyphenolic metabolites that may have negative effects on nutritional parameters, the chemical composition of sorghum grain polyphenol extracts from three commercial varieties (MR-Buster, Cracka, and Liberty) was determined through the use of an under-studied, alternative analytical approach involving Fourier-transform infrared (FT-IR) spectroscopy and direct ionization mass spectrometry. Supervised analyses and interrogation of the data contributing to variation resulted in the identification of a variety of metabolites, including established polyphenols, lignin-like anti-nutrients, and complex sugars, as well as high levels of fatty acids which could contribute to nutritional variation and underperformance in monogastrics. FT-IR and mass spectrometry could both discriminate among the different sorghum varieties indicating that FT-IR, rather than more sophisticated chromatographic and mass spectrometric methods, could be incorporated into quality control applications.

Survey of the year 2008: applications of isothermal titration calorimetry.

Isothermal titration calorimetry (ITC) is a fast, accurate and label-free method for measuring the thermodynamics and binding affinities of molecular associations in solution. Because the method will measure any reaction that results in a heat change, it is applicable to many different fields of research from biomolecular science, to drug design and materials engineering, and can be used to measure binding events between essentially any type of biological or chemical ligand. ITC is the only method that can directly measure binding energetics including Gibbs free energy, enthalpy, entropy and heat capacity changes. Not only binding thermodynamics but also catalytic reactions, conformational rearrangements, changes in protonation and molecular dissociations can be readily quantified by performing only a small number of ITC experiments. In this review, we highlight some of the particularly interesting reports from 2008 employing ITC, with a particular focus on protein interactions with other proteins, nucleic acids, lipids and drugs. As is tradition in these reviews we have not attempted a comprehensive analysis of all 500 papers using ITC, but emphasize those reports that particularly captured our interest and that included more thorough discussions we consider exemplify the power of the technique and might serve to inspire other users.

Terahertz and far infrared spectroscopy of alanine-rich peptides having variable ellipticity.

Terahertz spectra of four alanine-rich peptides with known secondary structures were studied by terahertz time domain spectroscopy (THz-TDS) and by Fourier transform infrared spectroscopy (FTIR) using a synchrotron light source and a liquid-helium cooled bolometer. At ambient temperatures the usable bandwidth was restricted to 0.2-1.5 THz by the absorbance of water. The existence of a solvation shell around the peptide in solution was observed and its size estimated to be between 11 and 17 Å. By cooling the peptide solution to 80 K in order to reduce the water absorbance the bandwidth was increased to 0.1-3.0 THz for both THz-TDS and FTIR. Spectra were consistent with monotonic absorbance of the peptide and the existence of a solid amorphous low density solvation shell.

The use of catechins in Chinese hamster ovary cell media for the improvement of monoclonal antibody yields and a reduction of acidic species.

Catechin compounds have potential benefits for recombinant monoclonal antibody (Mab) production as chemical additives in cell culture media. In this study, four catechin compounds catechin (Cat), epicatechin (EC), gallocatechin-gallate (GCG), and epigallocatechin-gallate (EGCG) were added to cell culture media (at 50 µM) and their effects on the recombinant Chinese hamster ovary (CHO) cell culture, specific productivity, and Mab quality were assessed. The results indicate that the improvement of specific productivity was linked to cell growth inhibition. All catechins caused cell phase growth arrest by lowering the number of cells in the G1/G0 phase and increasing the cells in the S and G2/M phases. Late addition of the catechin resulted in a significantly higher final IgG concentration. Cat and EC caused an improvement in the final antibody titer of 1.5 ± 0.1 and 1.3 ± 0.1 fold, respectively. Catechins with a galloyl group (GCG and EGCG) arrested cell growth and reduced cell specific productivity at the concentrations tested. The Cat-treated IgG was found to have reduced acidic species with a corresponding increase in the main peak.

Resveratrol addition to Chinese hamster ovary cell culture media: The effect on cell growth, monoclonal antibody synthesis, and its chemical modification.

The effect of the addition of resveratrol to cell culture media during the production of monoclonal antibodies was investigated. Treatments of Chinese hamster ovary (CHO) cells expressing immunoglobulin G (IgG) with 25 and 50 µM resveratrol showed that resveratrol was capable of slowing cell growth while almost doubling cell-specific productivity to 4.7 ± 0.6 pg IgG/cell·day, resulting in up to a 1.37-fold increase of the final IgG titer. A resveratrol concentration of 50 µM slowed the progression through the cell cycle temporarily by trapping cells in the S-phase. Cation exchange chromatography showed no significant difference in the composition of acidic or basic IgG species and size exclusion chromatography indicated no change in fragmentation or aggregation of the recombinant IgG in the treatment groups. Resveratrol could be used as a chemical additive to CHO media where it would enhance IgG productivity and provide a degree of protection against hydroxyl and superoxide free radicals, expanding the range of options for process improvement available to monoclonal antibody manufacturers.

Terahertz spectroscopic differentiation of microstructures in protein gels.

We demonstrate that terahertz (THz) spectroscopy can be used to differentiate soft protein microstructures. Differentiation of soft microstructures in gels has to date been performed using optical imaging techniques (e.g. electron microscope), but a non-destructive differentiation tool is lacking. Particulate and fine-stranded (fibrillar) soft protein microstructures are of interest, particularly to medical researchers, because they form from naturally occurring proteins that are thought to be involved in several human diseases, such as Alzheimer's disease. In this study, globular beta-lactoglobulin structures with diameters of 2 microm, and fibrillar structures with diameters less than 0.03 microm are observed between 0.8 and 1.5 THz. Results show that the globular structures have a decline in THz transmission when compared to the fibrillar ones. The cause of this decline is possibly due to Rayleigh scattering from the globular microstructures.

Advances in liquid formulations of parenteral therapeutic proteins.

Liquid formulation of therapeutic proteins is a maturing technology. Demand for products that are easy to use in the clinic or that are amenable to self-administration make a ready to use liquid formulation desirable. Most modern liquid formulations have a simple composition; comprising a buffer, a tonicity modifier, a surfactant, sometimes a stabiliser, the therapeutic protein and water. Recent formulations of monoclonal antibodies often use histidine or acetate as the buffer, sucrose or trehalose as the tonicity modifier and polysorbate 20 or 80 as the surfactant with a pH of 5.7 +/- 0.4. The mechanisms for the behaviour of excipients is still debated by academics so formulation design is still a black art. Fortunately, a statistical approach like design of experiment is suitable for formulation development and has been successful when combined with accelerated stability experimentation. The development of prefilled syringes and pens has added low viscosity and shear resistance to the quality attributes for a successful formulation. To achieve patient compliance for self-administration, formulations that cause minimal pain and tissue damage is also desirable.

Screening Naturally Occurring Phenolic Antioxidants for Their Suitability as Additives to CHO Cell Culture Media Used to Produce Monoclonal Antibodies.

This study identified several antioxidants that could be used in Chinese hamster ovary (CHO)cell culture media and benefit monoclonal antibody production. The flavan-3-ols, catechin, epicatechin, epigallocatechin gallate and gallocatechin gallate all had no detrimental effect on cell viability at the concentrations tested, and they reduced the final viable cell count with a resulting rise in the cell specific productivity. The flavone, luteolin behave similarly to the flavan-3-ols. Resveratrol at 50 µM concentration resulted in the most pronounced reduction in viable cell density with minimal decrease in IgG synthesis and the largest increase in cell specific productivity. Low concentrations of α-tocopherol (35 µM) reduced viable cell density and raised cell specific productivity, but at higher concentration it had little additional effect. As high concentrations of α-tocopherol are not toxic to CHO cells, its addition as an anti-oxidant has great potential. Kaempferol up to 50 µM, curcumin up to 20 µM and piceid up to 100 µM showed little effect on growth or IgG synthesis and could be useful as antioxidants. Caffeic acid phenethyl ester was toxic to CHO cell and of no interest. Seven of the phenolic compounds tested are potential cell cycle inhibitors as well as having intrinsic antioxidant properties.