An Application of Ultraviolet Spectroscopy to Study Interactions in Proteins Solutions at High Concentrations

Quantifying Protein Shape to Elucidate Its Influence on Solution Viscosity in High-Concentration Electrolyte Solutions

Therapeutic proteins with a high concentration and low viscosity are highly desirable for subcutaneous and certain local injections. The shape of a protein is known to influence solution viscosity; however, the precise quantification of protein shape and its relative impact compared to other factors like charge-charge interactions remains unclear. In this study, we utilized seven model proteins of varying shapes and experimentally determined their shape factors (v) based on Einstein's viscosity theory, which correlate strongly with the ratios of the proteins' surface area to the 2/3 power of their respective volumes, based on protein crystal structures resolved experimentally or predicted by AlphaFold. This finding confirms the feasibility of computationally estimating protein shape factors from amino acid sequences alone. Furthermore, our results demonstrated that, in high-concentration electrolyte solutions, a more spherical protein shape increases the protein's critical concentration (C*), the transition concentration beyond which protein viscosity increases exponentially relative to concentration increases. In summary, our work elucidates protein shape as a key determinant of solution viscosity through quantitative analysis and comparison with other contributing factors. This provides insights into molecular engineering strategies to optimize the molecular design of therapeutic proteins, thus optimizing their viscosity.

Computational and physicochemical insight into 4-hydroxy-2-nonenal induced structural and functional perturbations in human low-density lipoprotein

Lipid peroxidation (LPO) is a biological process that frequently occurs under physiological conditions. Undue oxidative stress increases the level of LPO; which may further contribute to the development of cancer. 4-Hydroxy-2-nonenal (HNE), one of the principal by-products of LPO, is present in high concentrations in oxidatively stressed cells. HNE rapidly reacts with various biological components, including DNA and proteins; however, the extent of protein degradation by lipid electrophiles is not well understood. The influence of HNE on protein structures will likely have a considerable therapeutic value. This research elucidates the potential of HNE, one of the most researched phospholipid peroxidation products, in modifying low-density lipoprotein (LDL). In this study, we tracked the structural alterations in LDL by HNE using various physicochemical techniques. To comprehend the stability, binding mechanism and conformational dynamics of the HNE-LDL complex, computational investigations were carried out. LDL was altered in vitro by HNE, and the secondary and tertiary structural alterations were examined using spectroscopic methods, such as UV-visible, fluorescence, circular dichroism and fourier transform infrared spectroscopy. Carbonyl content, thiobarbituric acid-reactive-substance (TBARS) and nitroblue tetrazolium (NBT) reduction assays were used to examine changes in the oxidation status of LDL. Thioflavin T (ThT), 1-anilinonaphthalene-8-sulfonic (ANS) binding assay and electron microscopy were used to investigate aggregates formation. According to our research, LDL modified by HNE results in changes in structural dynamics, oxidative stress and the formation of LDL aggregates. The current investigation must characterize HNE's interactions with LDL and comprehend how it can change their physiological or pathological functions.Communicated by Ramaswamy H. Sarma.

Protein Nucleation and Crystallization Process with Process Analytical Technologies in a Batch Crystallizer

Protein crystallization has drawn great attention to replacing the traditional downstream processing for protein-based pharmaceuticals due to its advantages in stability, storage, and delivery. Limited understanding of the protein crystallization processes requires essential information based on real-time tracking during the crystallization process. A batch crystallizer of 100 mL fitted with a focused beam reflectance measurement (FBRM) probe and a thermocouple was designed for in situ monitoring of the protein crystallization process, with simutaneously record of off-line concentrations and crystal images. Three stages in the protein batch crystallization process were identified: long-period slow nucleation, rapid crystallization, and slow growth and breakage. The induction time was estimated by FBRM, i.e., increasing numbers of particles in the solution, which could be half of the time required for detecting the decrease of the concentration, by offline measurement. The induction time decreased with an increase in supersaturation within the same salt concentration. The interfacial energy for nucleation was analyzed based on each experimental group with equal salt concentration and different concentrations of lysozyme. The interfacial energy reduced with an increase in salt concentration in the solution. The yield of the experiments was significantly affected by the protein and salt concentrations and could achieve up to 99% yield with a 26.5 μm median crystal size upon stabilized concentration readings.

Rutin impedes human low-density lipoprotein from non-enzymatic glycation: A mechanistic insight against diabetes-related disorders

Glycation of human low-density protein (LDL) has an essential contribution to cardiovascular diseases. Natural compounds like rutin have been extensively studied in preventing glycation-induced oxidative stress. This study examined rutin's anti-glycation potential with glycated LDL utilizing spectroscopic and in silico methods. Glycated LDL treated with rutin, showed around 80 % inhibition in advanced glycation end-product production. Carbonyl content and lipid peroxidation like assays were used to establish the development of oxidative stress. Rutin was seen to lower the generation of oxidative stress in a dose-dependent manner. Using thioflavin t-test and electron microscopy, rutin was suggested to restore the structural disturbances in glycated LDL. Moreover, CD spectroscopy suggested reinstation of secondary structure of glycated LDL treated with rutin. Mechanistic insights between rutin and LDL were observed through spectroscopic measures. Molecular docking study confirmed the LDL-rutin binding with a binding energy of -10.0 kcal/mol. The rutin-LDL complex was revealed to be highly stable by molecular dynamics simulation, with RMSD, RMSF, Rg, SASA, and the secondary structure of LDL remaining essentially unchanged during the simulation period. Our study suggests that rutin possesses strong anti-glycating properties, which can be useful in therapeutics, as glycated LDL has an important role in atherosclerotic cardiovascular diseases.

Effect of crocin on glycated human low-density lipoprotein: A protective and mechanistic approach

Human low-density lipoprotein (LDL) is known to have a role in coronary artery diseases when it undergoes modification due to hyperglycaemic conditions. Plant products like crocin play an essential role in protecting against oxidative stress and in the production of advanced glycation end-products (A.G.E.s). In this study, the anti-glycating effect of crocin was analyzed using various biochemical, spectroscopic, and in silico approaches. Glycation-mediated oxidative stress was confirmed by nitroblue tetrazolium, carbonyl content, and lipid peroxidation assays, and it was efficiently protected by crocin in a concentration-dependent manner. A.N.S. fluorescence, thioflavin T (ThT) assay, and electron microscopy confirmed that the structural changes in LDL during glycation lead to the formation of fibrillar aggregates, which can be minimized by crocin treatment. Moreover, secondary structural perturbations in LDL were observed using circular dichroism (CD) and Fourier transform infrared spectroscopy (FTIR), where crocin was found to prevent the loss of secondary structure in glycated LDL. Spectroscopic studies like U.V. absorbance, fluorescence spectroscopy, CD, FTIR, and fluorescence resonance energy transfer (FRET) provided insights into the interaction mechanism between LDL and crocin. Molecular docking supports these results with a highly negative binding energy of -10.3 kcal/mol, suggesting the formation of a stable ldl-crocin complex. Our study indicates that crocin may be a potent protective agent against coronary artery diseases by limiting the glycation of LDL in people with such disorders.

Comparative evaluation of biomedical and phytochemical applications of zinc nanoparticles by using Fagonia cretica extracts

The use of the green approach for nanoparticle synthesis yielded noticeable concern due to its eco-friendliness, cost-effectiveness, and reduced production of toxic chemicals. The current study was designed to formulate Zinc oxide nanoparticles (ZnO NPs) by using Fagonia cretica extracts, evaluating its phytochemical content, and different biological activities. Four different solvents; methanol (MeOH), n-Hexane (n–H), aqueous (Aq), and ethyl acetate (EA), had been utilized in the extracting method. ZnO NPs were successfully synthesized and characterized by UV–vis spectroscopy and scanning electron microscopy (SEM). The UV–vis spectra showed absorbance peaks between 350–400 nm range and SEM analysis revealed spherical morphology with particle sizes ranging from 65–80 nm. In phytochemical analysis, crude extracts exhibited the highest phytochemical content as they contain enriched secondary metabolites. n-hexane extract showed the highest phenolic contents while aqueous extracts showed the highest flavonoid content. Maximum free radicle scavenging activity was observed in NPs synthesized from ethyl-acetate extract with an IC₅₀ value of 35.10 µg/ml. Significant antibacterial activity was exhibited by NPs polar solvents against K. pneumonae, E. coli, and B. subtilis. Polar solvents showed considerable antifungal potential against A. flavus and F. solani. NPs synthesized from nH extract showed potential cytotoxic activity with an LC₅₀ value of 42.41 µg/ml against brine shrimps. A noteworthy antidiabetic activity was exhibited by nanoparticles synthesized from methanol extract i.e., 52.61 ± 0.36%. Significant bald zones were observed in nanoparticles synthesized from methanol extract rendering protein kinase inhibition. The present study highlights the significance of F. indica as a natural source for synthesizing functional nanoparticles with substantial antioxidant, antimicrobial, cytotoxic, protein kinase inhibitory, and antidiabetic properties.

Comparative Evaluation of Biomedical Applications of Zinc Nanoparticles Synthesized by Using Withania somnifera Plant Extracts

Green synthesis of metal nanoparticles is of great importance in the modern health care system. In this study, zinc nanoparticles (ZnONPs) were synthesized using leaf and root extracts of Withania somnifera using four different solvents. ZnONPs were characterized by UV-vis spectrophotometer with a range between 350–400 nm. Scanning electron microscope revealed spherical morphology with an overall size of 70–90 nm and XRD pattern confirmed the crystalline structure. The total flavonoids, phenolic, and alkaloid contents were significantly greater in the crude extracts as compared to ZnONPs. The highest scavenging activity was observed in ZnONPs from n-hexane and ethyl-acetate extracts of roots with IC₅₀ values of 27.36 µg/mL and 39.44 µg/mL, respectively. ZnONPs from methanol and aqueous extracts showed significant antibacterial activity against Escherichia coli, Staphylococcus aureus, and Bacillus subtilis while none of the extracts were found to have significant antifungal activity. Maximum cytotoxic activity was observed in ZnONPs synthesized from aqueous and n-hexane root extracts with LC₅₀ values of 9.36 µg/mL and 18.84 µg/mL, respectively. The highest antidiabetic potential was exhibited by ZnONPs from n-hexane leaf extracts, i.e., 47.67 ± 0.25%. Maximum protein kinase inhibitory potential was observed in ZnONPs of ethyl-acetate extract of roots with a bald zone of 12 mm. These results indicated that Withania somnifera-based ZnONPs showed significant biological activities compared to crude extracts. These findings can further be utilized for in-vivo analysis of nano-directed drug delivery systems.

ATR-FTIR spectroscopy and spectroscopic imaging for the analysis of biopharmaceuticals

Attenuated Total Reflection Fourier Transform Infrared (ATR-FTIR) spectroscopy is a label-free, non-destructive technique that can be applied to a vast range of biological applications, from imaging cancer tissues and live cells, to determining protein content and protein secondary structure composition. This review summarises the recent advances in applications of ATR-FTIR spectroscopy to biopharmaceuticals, the application of this technique to biosimilars, and the current uses of FTIR spectroscopy in biopharmaceutical production. We discuss the use of ATR-FTIR spectroscopic imaging to investigate biopharmaceuticals, and finally, give an outlook on the possible future developments and applications of ATR-FTIR spectroscopy and spectroscopic imaging to this field. Throughout the review comparisons will be made between FTIR spectroscopy and alternative analytical techniques, and areas will be identified where FTIR spectroscopy could perhaps offer a better alternative in future studies. This review focuses on the most recent advances in the field of using ATR-FTIR spectroscopy and spectroscopic imaging to characterise and evaluate biopharmaceuticals, both in industrial and academic research based environments.

Segregated Nanocompartments Containing Therapeutic Enzymes and Imaging Compounds within DNA-Zipped Polymersome Clusters for Advanced Nanotheranostic Platform

Nanotheranostics is an emerging field that brings together nanoscale-engineered materials with biological systems providing a combination of therapeutic and diagnostic strategies. However, current theranostic nanoplatforms have serious limitations, mainly due to a mismatch between the physical properties of the selected nanomaterials and their functionalization ease, loading ability, or overall compatibility with bioactive molecules. Herein, a nanotheranostic system is proposed based on nanocompartment clusters composed of two different polymersomes linked together by DNA. Careful design and procedure optimization result in clusters segregating the therapeutic enzyme human Dopa decarboxylase (DDC) and fluorescent probes for the detection unit in distinct but colocalized nanocompartments. The diagnostic compartment provides a twofold function: trackability via dye loading as the imaging component and the ability to attach the cluster construct to the surface of cells. The therapeutic compartment, loaded with active DDC, triggers the cellular expression of a secreted reporter enzyme via production of dopamine and activation of dopaminergic receptors implicated in atherosclerosis. This two-compartment nanotheranostic platform is expected to provide the basis of a new treatment strategy for atherosclerosis, to expand versatility and diversify the types of utilizable active molecules, and thus by extension expand the breadth of attainable applications.

The Native Monomer of Bacillus Pumilus Ribonuclease Does Not Exist Extracellularly

Supported by crystallography studies, secreted ribonuclease of Bacillus pumilus (binase) has long been considered to be monomeric in form. Recent evidence obtained using native polyacrylamide gel electrophoresis and size-exclusion chromatography suggests that binase is in fact dimeric. To eliminate ambiguity and contradictions in the data we have measured conformational changes, hypochromic effect, and hydrodynamic radius of binase. The immutability of binase secondary structure upon transition from low to high protein concentration was registered, suggesting the binase dimerization immediately after translocation through the cell membrane and leading to detection of binase dimers only in the culture fluid regardless of ribonuclease concentration. Our results made it necessary to take a fresh look at the binase stability and cytotoxicity towards virus-infected or tumor cells.

Accurate and Rapid Protein Concentration Measurement of In-Process, High Concentration Protein Pools

Protein concentration is a critical product quality attribute and required for any therapeutic protein. Many commercial and investigational new biologics are now formulated at high concentrations (>100 mg/ml) to achieve successful subcutaneous administration. Assaying protein concentration in high concentration formulations poses a challenge, as traditional absorption spectroscopy and UPLC/HPLC (ultra/high performance liquid chromatography) assays cannot accurately measure such high concentrations without further solution manipulation. However, recent advances in UV/vis technology have led to the creation of instruments that measure samples at relatively short (<1 cm) path lengths, which would allow them to accurately measure high concentration protein samples in accordance with Beer Lambert Law principles. In this research, samples of five different proteins at concentrations ranging from 0.15 to 242 mg/ml (corresponding to OD280 vales of 0.15-315 AU) were measured on two different instruments employing different techniques of low path length UV/vis measurements. In order for the techniques to meet MSD's acceptance criteria for release assays, measurements were required to be accurate to within 10% of a reference measurement (performed on a traditional UV/vis spectrophotometer) and to be precise within 5% CV. The results show that using a technique known as slope spectroscopy, it is possible to measure OD280 from 0.5 to 315 AU with <7% error relative to the reference measurement. If instead measurements are taken using an instrument utilizing a single, small path length, it is possible to measure absorbances from 0.2 to ~75 AU with <7% error. This article concludes that the slope spectroscopy technique performed within the acceptance criteria across the full range of measured absorbances and that the single, short path length measurement performed within the acceptance criteria up to 75 AU.

Spectroscopic methods for assessing the molecular origins of macroscopic solution properties of highly concentrated liquid protein solutions

In cases of subcutaneous injection of therapeutic monoclonal antibodies, high protein concentrations (>50 mg/ml) are often required. During the development of these high concentration liquid formulations (HCLF), challenges such as aggregation, gelation, opalescence, phase separation, and high solution viscosities are more prone compared to low concentrated protein formulations. These properties can impair manufacturing processes, as well as protein stability and shelf life. To avoid such unfavourable solution properties, a detailed understanding about the nature of these properties and their driving forces are required. However, the fundamental mechanisms that lead to macroscopic solution properties, as above mentioned, are complex and not fully understood, yet. Established analytical methods for assessing the colloidal stability, i.e. the ability of a native protein to remain dispersed in solution, are restricted to dilute conditions and provide parameters such as the second osmotic virial coefficient, B₂₂, and the diffusion interaction coefficient, k_D. These parameters are routinely applied for qualitative estimations and identifications of proteins with challenging solution behaviours, such as high viscosities and aggregation, although the assays are prepared for low protein concentration conditions, typically between 0.1 and 20 mg/ml ("ideal" solution conditions). Quantitative analysis of samples of high protein concentration is difficult and it is hard to obtain information about the driving forces of such solution properties and corresponding protein-protein self-interactions. An advantage of using specific spectroscopic methods is the potential of directly analysing highly concentrated protein solutions at different solution conditions. This allows for collecting/gaining valuable information about the fundamental mechanisms of solution properties of the high protein concentration regime. In addition, the derived parameters might be more predictive as compared to the parameters originating from assays which are optimized for the low protein concentration range. The provided information includes structural data, molecular dynamics at various timescales and protein-solvent interactions, which can be obtained at molecular resolution. Herein, we provide an overview about spectroscopic techniques for analysing the origins of macroscopic solution behaviours in general, with a specific focus on pharmaceutically relevant high protein concentration and formulation conditions.

In situ ultra-fast heat deposition does not perturb the structure of serum albumin

MnTPPS is a metallic water soluble porphyrin with high potential to be used as a contrast agent in photoacoustic tomography. In order to fully understand the interaction between MnTPPS and serum albumin and to investigate the effect of the light induced fast in situ heat deposition by MnTPPS in the protein, we performed several experimental studies using fluorescence and circular dichroism spectroscopies, as well as photoacoustic calorimetry. To identify the possible binding site(s) of the metalloporphyrin in serum albumin and to help interpret the spectroscopic results, a molecular docking exercise was also carried out. The fluorescence data indicate a 1 : 1 stoichiometry for the complex BSA : MnTPPS. The molecular docking results suggest one binding site at the subdomain IB of albumin, where Trp-134 is found, as the main binding site for MnTPPS. The CD data indicate no significant conformational changes of the BSA secondary structure upon MnTPPS binding and even after several minutes of laser excitation of MnTPPS. TR-PAC results show that the in situ heat deposition from MnTPPS does not cause any significant transient conformational change to the BSA structure. In conclusion, this work demonstrates that MnTPPS, in addition to the necessary physical and chemical properties to be used as a contrast agent in photoacoustic tomography, can be effectively carried by albumin and that in situ heat release following light absorption does not cause any significant damage to the protein structure.

Characterization of highly concentrated antibody solution - A toolbox for the description of protein long-term solution stability

High protein titers are gaining importance in biopharmaceutical industry. A major challenge in the development of highly concentrated mAb solutions is their long-term stability and often incalculable viscosity. The complexity of the molecule itself, as well as the various molecular interactions, make it difficult to describe their solution behavior. To study the formulation stability, long- and short-range interactions and the formation of complex network structures have to be taken into account. For a better understanding of highly concentrated solutions, we combined established and novel analytical tools to characterize the effect of solution properties on the stability of highly concentrated mAb formulations. In this study, monoclonal antibody solutions in a concentration range of 50-200 mg/ml at pH 5-9 with and without glycine, PEG4000, and Na2SO4 were analyzed. To determine the monomer content, analytical size-exclusion chromatography runs were performed. ζ-potential measurements were conducted to analyze the electrophoretic properties in different solutions. The melting and aggregation temperatures were determined with the help of fluorescence and static light scattering measurements. Additionally, rheological measurements were conducted to study the solution viscosity and viscoelastic behavior of the mAb solutions. The so-determined analytical parameters were scored and merged in an analytical toolbox. The resulting scoring was then successfully correlated with long-term storage (40 d of incubation) experiments. Our results indicate that the sensitivity of complex rheological measurements, in combination with the applied techniques, allows reliable statements to be made with respect to the effect of solution properties, such as protein concentration, ionic strength, and pH shift, on the strength of protein-protein interaction and solution colloidal stability.

Identification of gallic acid based glycoconjugates as a novel tubulin polymerization inhibitors

A novel class of gallic acid based glycoconjugates were designed and synthesized as potential anticancer agents. Among all the compounds screened, compound 2a showed potent anticancer activity against breast cancer cells. The latter resulted in tubulin polymerization inhibition and induced G2/M cell cycle arrest, generation of reactive oxygen species, mitochondrial depolarization and subsequent apoptosis in breast cancer cells. In addition, ultraviolet-visible spectroscopy and fluorescence quenching studies of the compound with tubulin confirmed direct interaction of compounds with tubulin. Molecular modeling studies revealed that it binds at the colchicine binding site in tubulin. Further, 2a also exhibited potent in vivo anticancer activity in LA-7 syngeneic rat mammary tumor model. Current data projects its strong candidature to be developed as anticancer agent.