Analytical Techniques for Structural Characterization of Proteins in Solid Pharmaceutical Forms: An Overview

Deep Learning-Powered Colloidal Digital SERS for Precise Monitoring of Cell Culture Media

Maintaining consistent quality in biomanufacturing is essential for producing high-quality complex biologics. Yet, current process analytical technologies (PAT) often fall short in achieving rapid and accurate monitoring of small-molecule critical process parameters and critical quality attributes. Surface-enhanced Raman spectroscopy (SERS) holds great promise but faces challenges like intensity fluctuations, compromising reproducibility. Herein, we propose a deep learning-powered colloidal digital SERS platform. This innovation converts SERS spectra into binary "ON/OFF" signals based on defined intensity thresholds, which allows single-molecule event visualization and reduces false positives. Through integration with deep learning, this platform enables detection of a broad range of analytes, unlimited by the lack of characteristic SERS peaks. Furthermore, we demonstrate its accuracy and reproducibility for studying AMBIC 1.1 mammalian cell culture media. These results highlight its rapidity, accuracy, and precision, paving the way for widespread adoption and scale-up as a novel PAT tool in biomanufacturing and diagnostics.

Polymeric Microneedles for Transdermal Delivery of Human Placental Tissue for the Treatment of Osteoarthritis

Biologics targeting matrix-degrading proteases, cartilage repair, and inflammation are emerging as promising approaches for osteoarthritis (OA) treatment. Recent research highlights biologic-human placental tissue (HPT) as a potential OA therapy due to its biocompatibility, abundant protein biofactors, and ability to reduce cartilage degradation by suppressing protease expression. Microneedles (MNs) are receiving growing attention for enhancing transdermal delivery of biologics as an alternative to conventional subcutaneous injections. The lyophilized human placental extract (LHP) loaded polymeric MNs are fabricated using a micromolding technique for transdermal delivery. Ex vivo release studies reveal that MNs exhibit a gradual and consistent release of LHP, indicating a sustained delivery profile. LHP-MNs are nontoxic and anti-inflammatory in nature against human skin cells and interleukin (IL-1β) induced synovial cells. Furthermore, the in vivo study shows that LHP-MNs substantially improve behavioral parameters in OA rat models and lower serum concentrations of tumor necrosis factor- α (TNF-α) and cartilage oligomeric matrix protein (COMP) biomarkers, thereby alleviating knee and ankle joint injuries. Histopathological analysis indicates that LHP-MNs significantly preserve cartilage integrity. The study results suggest that employing polymeric MNs for transdermal delivery of LHP can be a promising treatment approach for OA, with the added benefit of excellent patient compliance.

Enabling simultaneous photoluminescence spectroscopy and X-ray footprinting mass spectrometry to study protein conformation and interactions

X-ray footprinting mass spectrometry (XFMS) is a structural biology method that uses broadband X-rays for in situ hydroxyl radical labeling to map protein interactions and conformation in solution. However, while XFMS alone provides important structural information on biomolecules, as we move into the era of the interactome, hybrid methods are becoming increasingly necessary to gain a comprehensive understanding of protein complexes and interactions. Toward this end, we report the development of the first synergetic application of inline and real-time fluorescent spectroscopy at the Advanced Light Source's XFMS facility to study local protein interactions and global conformational changes simultaneously. To facilitate general use, we designed a flexible and optimum system for producing high-quality spectroscopy-XFMS hybrid data, with rapid interchangeable liquid jet or capillary sample delivery for multimodal inline spectroscopy, and several choices for optofluidic environments. To validate the hybrid system, we used the covalently interacting SpyCatcher-SpyTag split protein system. We show that our hybrid system can be used to detect the interaction of SpyTag and SpyCatcher via fluorescence resonance energy transfer (FRET), while elucidating key structural features throughout the complex at the residue level via XFMS. Our results highlight the usefulness of hybrid method in providing binding and structural details to precisely engineer protein interactions.

Deep Learning-Powered Colloidal Digital SERS for Precise Monitoring of Cell Culture Media

Maintaining consistent quality in biopharmaceutical manufacturing is essential for producing high-quality complex biologics. Yet, current process analytical technologies (PAT) struggle to achieve rapid and highly accurate monitoring of small molecule critical process parameters and critical quality attributes. While Raman spectroscopy holds great promise as a highly sensitive and specific bioanalytical tool for PAT applications, its conventional implementation, surface-enhanced Raman spectroscopy (SERS), is constrained by considerable temporal and spatial intensity fluctuations, limiting the achievable reproducibility and reliability. Herein, we introduce a deep learning-powered colloidal digital SERS platform to address these limitations. Rather than addressing the intensity fluctuations, the approach leverages their very stochastic nature, arising from highly dynamic analyte-nanoparticle interactions. By converting the temporally fluctuating SERS intensities into digital binary "ON/OFF" signals using a predefined intensity threshold by analyzing the characteristic SERS peak, this approach enables digital visualization of single-molecule events and significantly reduces false positives and background interferences. By further integrating colloidal digital SERS with deep learning, the applicability of this platform is significantly expanded and enables detection of a broad range of analytes, unlimited by the lack of characteristic SERS peaks for certain analytes. We further implement this approach for studying AMBIC 1.1, a chemically-defined, serum-free complete media for mammalian cell culture. The obtained highly accurate and reproducible results demonstrate the unique capabilities of this platform for rapid and precise cell culture media monitoring, paving the way for its widespread adoption and scaling up as a new PAT tool in biopharmaceutical manufacturing and biomedical diagnostics.

Demonstration of physicochemical and functional similarity between Stimufend (pegfilgrastim-fpgk) and Neulasta (pegfilgrastim): A comparative analytical assessment

BACKGROUND

Pegfilgrastim is a long-acting recombinant human granulocyte colony-stimulating factor biologic that is indicated to reduce the incidence of infections, manifested by febrile neutropenia, in patients receiving myelosuppressive anti-cancer drugs and to increase survival in patients acutely exposed to myelosuppressive doses of radiation. Due to the high cost of biologic therapy and the scarcity of biosimilar alternatives, there is an unmet medical need for targeted biologics.

OBJECTIVE

This comparative analytical investigation aimed to confirm the similarity of biosimilar Stimufend® (pegfilgrastim-fpgk) to reference product Neulasta® (pegfilgrastim).

METHODS

The analysis was designed using state-of-the-art orthogonal techniques and side-by-side testing to compare the physicochemical and biological properties of these two products. The measured quality attributes included the primary structure and higher order structure of the molecule, purity/impurity profiles, product variants, process-related impurities, composition, content, and biological activity. The statistical analysis was based on risk ranking of the critical quality attributes (very low, low, moderate, high, very high), and scientific considerations in combination with the characteristics of the assay (sensitivity, selectivity, and variability). In addition, non-quantitative parameters were compared using a descriptive assessment of the product profile. Analytical similarity was concluded by quality attributes falling within the defined range of the originator product.

RESULTS

The results of this study confirm that Stimufend® is biosimilar to Neulasta® for all measured quality attributes. There are no clinically significant differences between Stimufend® and Neulasta®, which was confirmed by the marketing approval for Stimufend® by the Food and Drug Administration and the European Medicines Agency.

CONCLUSION

The findings of this study provide robust evidence supporting the structural and functional biosimilarity between Stimufend® and Neulasta®.

Luminescence "Turn-On" Sensing of Brain Natriuretic Peptide (BNP) - Dilated Cardiomyopathy Biomarker Based on the MoS2 Nanosheet Quenched Terbium Citrate Complex

Dilated cardiomyopathy (DCM), known as myocardial metabolic dysfunction, is recognized as a clinical condition characterized by left ventricular dilation or improper contraction of cardiac muscles in the absence of coronary atherosclerosis and hypertension. It is an independent risk factor for cardiac function caused by a hyperglycemic condition in diabetic patients leading to heart failure (HF), which renders the early diagnosis of DCM highly challenging. Hence, detection of early diagnostic biomarkers in blood serum to identify DCM conditions is quite requisite. Brain natriuretic peptide (BNP) is a well-recognized biomarker for heart failure and reported as an early diagnostic biomarker for DCM. In this work, we developed a terbium citrate based MoS2 nanosheet (NS) coupled immunoprobe for the sensitive detection of BNP. The antibody conjugated Tb-citrate complex exhibits green fluorescence, which is quenched by the introduction of MoS2 NS. On subsequent addition of antigen BNP, the fluorescence is enhanced because of specific antigen-antibody interaction. The probe is selective and sensitive toward BNP in a linear range from 30.76 to 849.85 pg/mL with a low LOD of 3.87 pg/mL. The probe is validated in spiked human serum samples with good recovery percentage.

Evaluating larvicidal, ovicidal and growth inhibiting activity of five medicinal plant extracts on Culex pipiens (Diptera: Culicidae), the West Nile virus vector

Mosquitoes, one of the deadliest animals on the planet, cause millions of fatalities each year by transmitting several human illnesses. Synthetic pesticides were previously used to prevent the spread of diseases by mosquitoes, which was effective in protecting humans but caused serious human health problems, environmental damage, and developed mosquito pesticide resistance. This research focuses on exploring new, more effective, safer, and environmentally friendly compounds to improve mosquito vector management. Phytochemicals are possible biological agents for controlling pests and many are target-specific, rapidly biodegradable, and eco-friendly. The potential of extracts of Lantana camara, Melia azedarach, Nerium oleander, Ricinus communis, and Withania somnifera against 3rd instar Culex pipiens (Common house mosquito) larvae was evaluated. Methanol extracts had more toxic effects against Cx. pipiens larvae (95-100%, 24 h post-treatment) than aqueous extracts (63-91%, 24 h post-treatment). The methanol extracts of Nerium oleander (LC50 = 158.92 ppm) and Ricinus communis (LC50 = 175.04 ppm) were very effective at killing mosquito larvae, 24 h after treatment. N. oleander (LC50 = 373.29 ppm) showed high efficacy in aqueous plant extracts. Among the different extracts of the five plants screened, the methanol extract of R. communis recorded the highest ovicidal activity of 5% at 800 ppm concentration. Total developmental duration and growth index were highly affected by R. communis and M. azedarach methanol extracts. In field tests it was clear that plant extracts decreased mosquito larval density, especially when mixed with mosquito Bti briquette, with stability up to seven days for N. oleander. GC-MS results showed that the methanol extract had a higher number of chemical compounds, particularly with more terpene compounds. A high-performance liquid chromatography (HPLC) technique was used to detect the existence of non-volatile polyphenols and flavonoids. All five methanol extracts showed high concentrations of active ingredients such as gallic acid, chlorogenic acid (more than 100 μg/ml) and the rosmarinic acid was also found in all the five extracts in addition to 17 active polyphenols and flavonoids presented at moderate to low concentrations. Molecular modeling of 18 active ingredients detected by the HPLC were performed to the vicinity of one of the fatty acid binding proteins of lm-FABP (PDB code: 2FLJ). Rutin, Caffeic acid, coumaric acid and rosmarinic acid which presented densely in R. communis and N. oleander showed multiple and stable intermolecular hydrogen bonding and π-π stacking interactions. The inhibition ability of the fatty acid binding protein, FABP4, was evaluated with remarkable receptor inhibition evident, especially with R. communis and N. oleander having inhibitory concentrations of IC50 = 0.425 and 0.599 µg/mL, respectively. The active phytochemical compounds in the plants suggest promising larvicidal and ovicidal activity, and have potential as a safe and effective alternative to synthetic insecticides.

Proteomic Characterization of Human Placenta: Insights into Potential Therapeutic Applications for Osteoarthritis

Biologics have become increasingly prominent as therapeutics in recent years due to their innate immune-privileged nature, biocompatibility, and high levels of protein biofactors. The aim of the study is to characterise the biologic, lyophilized human placenta (LHP) and explore its therapeutic potential for osteoarthritis (OA). The presence of six bioactive constituents that regulate cell-extracellular matrix interaction was identified by liquid chromatography coupled to electrospray ionization and quadrupole time-of-flight mass spectrometry (LC-ESI-QTOF/MS). Metalloproteinase inhibitor 3 (TIMP3), alpha-1 anti-trypsin (a1AT), basic fibroblast growth factor (bFGF), and transforming growth factor β1 (TGFβ1) were detected and quantified using ELISA. The total protein content present in LHP by Bradford assay was found to be 409.35 ± 0.005 μg/ml. The analytical techniques such as Attenuated Total Reflectance-Fourier Transform Infrared spectroscopy (ATR-FTIR), solid state carbon-13 Nuclear Magnetic Resonance (ssC13 NMR) spectroscopy, and Differential Scanning Calorimetry (DSC) revealed the secondary structure and conformational stability of LHP. X-Ray diffraction (XRD) studies showed its amorphous nature. Bioactivity assessment of LHP was performed in human keratinocytes (HaCaT) and human dermal fibroblasts (HDF) by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. The LHP was highly proliferative against skin cells and non-toxic, based on the findings of the bioactivity assay. LHP has the potential to be used as a therapeutic agent for OA, as its characterisation unveiled its physical stability, significant concentration of bioactive components that are pertinent to cartilage repair and its conformational stability.

Crafting Docetaxel-Loaded Albumin Nanoparticles Through a Novel Thermal-Driven Self-Assembly/Microfluidic Combination Technology: Formulation, Process Optimization, Stability, and Bioavailability

Background

The commercial docetaxel (DTX) formulation causes severe side effects due to polysorbate 80 and ethanol. Novel surfactant-free nanoparticle (NP) systems are needed to improve bioavailability and reduce side effects. However, controlling the particle size and stability of NPs and improving the batch-to-batch variation are the major challenges.

Methods

DTX-loaded bovine serum albumin nanoparticles (DTX-BSA-NPs) were prepared by a novel thermal-driven self-assembly/microfluidic technology. Single-factor analysis and orthogonal test were conducted to obtain the optimal formulation of DTX-BSA-NPs in terms of particle size, encapsulation efficiency (EE), and drug loading (DL). The effects of oil/water flow rate and pump pressure on the particle size, EE, and DL were investigated to optimize the preparation process of DTX-BSA-NPs. The drug release, physicochemical properties, stability, and pharmacokinetics of NPs were evaluated.

Results

The optimized DTX-BSA-NPs were uniform, with a particle size of 118.30 nm, EE of 89.04%, and DL of 8.27%. They showed a sustained release of 70% over 96 hours and an increased stability. There were some interactions between the drug and excipients in DTX-BSA-NPs. The half-life, mean residence time, and area under the curve (AUC) of DTX-BSA-NPs increased, but plasma clearance decreased when compared with DTX.

Conclusion

The thermal-driven self-assembly/microfluidic combination method effectively produces BSA-based NPs that improve the bioavailability and stability of DTX, offering a promising alternative to traditional formulations.

Neutrophil-derived nanovesicles deliver IL-37 to mitigate renal ischemia-reperfusion injury via endothelial cell targeting

Renal ischemia-reperfusion injury (IRI) is one of the most important causes of acute kidney injury (AKI). Interleukin (IL)-37 has been suggested as a novel anti-inflammatory factor for the treatment of IRI, but its application is still limited by its low stability and delivery efficiency. In this study, we reported a novel engineered method to efficiently and easily prepare neutrophil membrane-derived vesicles (N-MVs), which could be utilized as a promising vehicle to deliver IL-37 and avoid the potential side effects of neutrophil-derived natural extracellular vesicles. N-MVs could enhance the stability of IL-37 and targetedly deliver IL-37 to damaged endothelial cells of IRI kidneys via P-selectin glycoprotein ligand-1 (PSGL-1). In vitro and in vivo evidence revealed that N-MVs encapsulated with IL-37 (N-MV@IL-37) could inhibit endothelial cell apoptosis, promote endothelial cell proliferation and angiogenesis, and decrease inflammatory factor production and leukocyte infiltration, thereby ameliorating renal IRI. Our study establishes a promising delivery vehicle for the treatment of renal IRI and other endothelial damage-related diseases.

Larvicidal activity of Acacia nilotica extracts against Culex pipiens and their suggested mode of action by molecular simulation docking

Mosquitoes are one of the deadliest and most hazardous animals on Earth, where they transmit several diseases that kill millions of people annually. There is an ongoing search almost everywhere in the world for more effective and contemporary ways to control mosquitoes other than pesticides. Phytochemicals are affordable, biodegradable biological agents that specialize in eliminating pests that represent a risk to public health. The effectiveness of Acacia nilotica methanol and aqueous leaf extracts against 4th instar larvae was evaluated. The results revealed that the methanol extract of A. nilotica had a noticeable influence on the mortality rate of mosquito larvae, especially at high concentrations. Not only did the mortality rate rise significantly, but the hatching of the mosquito eggs was potentially suppressed.Terpenes, fatty acids, esters, glycosides, pyrrolidine alkane, piperazine, and phenols were the most prevalent components in the methanol extract, while the aqueous extract of A. nilotica exclusively showed the presence of fatty acids. The insecticidal susceptibility tests of both aqueous and alcoholic extract of A. nilotica confirmed that the Acacia plant could serves as a secure and efficient substitute for chemical pesticides because of its promising effect on killing larvae and egg hatching delaying addition to their safety as one of the natural pesticides. Molecular docking study was performed using one of the crucial and life-controlling protein targets, fatty acid binding protein (FABP) and the most active ingredients as testing ligands to describe their binding ability. Most of the structurally related compounds to the co-crystallized ligand, OLA, like hexadecanoic acid furnished high binding affinity to the target protein with very strong and stable intermolecular hydrogen bonding and this is quite similar to OLA itself. Some other structural non-related compounds revealed extraordinarily strong binding abilities like Methoxy phenyl piperazine. Most of the binding reactivities of the majortested structures are due to high structure similarity between the positive control, OLA, and tested compounds. Such structure similarity reinforced with the binding abilities of some detected compounds in the A. nilotica extract could present a reasonable interpretation for its insecticidal activity via deactivating the FABP protein. The FABP4 enzyme inhibition activity was assessed for of both methanolic and aqueous of acacia plant extract and the inhibition results of methanol extract depicted noticeable potency if compared to orlistat, with half-maximal inhibitory concentration (IC50) of 0.681, and 0.535 µg/ml, respectively.

In-situ investigation of solid phase evolution during lyophilization of mannitol-based antibody formulations using an XRPD climate chamber

Crystalline mannitol is commonly used as bulking agent in antibody formulations to provide structure to the lyophilized cake and prevent collapse. Depending on the lyophilization process conditions mannitol can either crystallize as α-, β-, δ-mannitol, mannitol-hemihydrate, or transition to its amorphous state. While crystalline mannitol helps to create a firmer cake structure this is not true for amorphous mannitol. The hemihydrate is also an undesired physical form as it may reduce the drug product stability by releasing bound water molecules into the cake. Our aim was to simulate lyophilization processes in an X-ray powder diffraction (XRPD) climate chamber. In the climate chamber, the process can be carried out fast with low sample quantities to determine optimal process conditions. Insights on the emergence of desired anhydrous mannitol forms helps to adjust the process parameters in larger scale freeze-dryers. In our study we have identified the critical process steps for our formulations and then varied relevant process parameters, which were the annealing temperature, annealing time and temperature ramp rate of the freeze-drying process. Furthermore, the effect of the presence of antibodies on excipient crystallization was investigated by performing the studies on placebo solutions versus two respective antibody formulations. A comparison of the products obtained in a freeze-dryer and the simulated process in the climate chamber showed good accordance demonstrating the method as suitable tool to identify ideal process conditions on a laboratory scale.

Storage and Lyophilization of Pure Proteins

This chapter outlines empirical procedures for the storage of pure proteins with preservation of high levels of biological activity. It describes simple and workable means of preventing microbial contamination and proteolytic degradation and the use of various types of stabilizing additives. It sets out the principles of lyophilization (a complex process comprising freezing, primary drying, and secondary drying stages, otherwise known as freeze-drying). There follows a general procedure for the use of lyophilizer apparatus with emphasis on best practice and on pitfalls to avoid. The use of modulated differential scanning calorimetry to measure the glass transition temperature, a key parameter in the design and successful operation of lyophilization processes, is described. This chapter concludes with brief summaries of interesting recent work in the field.

Impact of process stress on protein stability in highly-loaded solid protein/PEG formulations from small-scale melt extrusion

As protein-based therapeutics often exhibit a limited stability in liquid formulations, there is a growing interest in the development of solid protein formulations due to improved protein stability in the solid state. We used small-scale (<3 g) ram and twin-screw extrusion for the solid stabilization of proteins (Lysozyme, BSA, and human insulin) in PEG-matrices. Protein stability after extrusion was systematically investigated using ss-DSC, ss-FTIR, CD spectroscopy, SEM-EDX, SEC, RP-HPLC, and in case of Lysozyme an activity assay. The applied analytical methods offered an accurate assessment of protein stability in extrudates, enabling the comparison of different melt extrusion formulations and process parameters (e.g., shear stress levels, screw configurations, residence times). Lysozyme was implemented as a model protein and was completely recovered in its active form after extrusion. Differences seen between Lysozyme- and BSA- or human insulin-loaded extrudates indicated that melt extrusion could have an impact on the conformational stability. In particular, BSA and human insulin were more susceptible to heat exposure and shear stress compared to Lysozyme, where shear stress was the dominant parameter. Consequently, ram extrusion led to less conformational changes compared to TSE. Ram extrusion showed good protein particle distribution resulting in the preferred method to prepare highly-loaded solid protein formulations.

Protein Function Analysis through Machine Learning

Machine learning (ML) has been an important arsenal in computational biology used to elucidate protein function for decades. With the recent burgeoning of novel ML methods and applications, new ML approaches have been incorporated into many areas of computational biology dealing with protein function. We examine how ML has been integrated into a wide range of computational models to improve prediction accuracy and gain a better understanding of protein function. The applications discussed are protein structure prediction, protein engineering using sequence modifications to achieve stability and druggability characteristics, molecular docking in terms of protein-ligand binding, including allosteric effects, protein-protein interactions and protein-centric drug discovery. To quantify the mechanisms underlying protein function, a holistic approach that takes structure, flexibility, stability, and dynamics into account is required, as these aspects become inseparable through their interdependence. Another key component of protein function is conformational dynamics, which often manifest as protein kinetics. Computational methods that use ML to generate representative conformational ensembles and quantify differences in conformational ensembles important for function are included in this review. Future opportunities are highlighted for each of these topics.

Biopharmaceutical nanoclusters: Towards the self-delivery of protein and peptide therapeutics

Protein and peptide biopharmaceuticals have had a major impact on the treatment of a number of diseases. There is a growing interest in overcoming some of the challenges associated with biopharmaceuticals, such as rapid degradation in physiological fluid, using nanocarrier delivery systems. Biopharmaceutical nanoclusters (BNCs) where the therapeutic protein or peptide is clustered together to form the main constituent of the nanocarrier system have the potential to mimic the benefits of more established nanocarriers (e.g., liposomal and polymeric systems) whilst eliminating the issue of low drug loading and potential side effects from additives. These benefits would include enhanced stability, improved absorption, and increased biopharmaceutical activity. However, the successful development of BNCs is challenged by the physicochemical complexity of the protein and peptide constituents as well as the dynamics of clustering. Here, we present and discuss common methodologies for the synthesis of therapeutic protein and peptide nanoclusters, as well as review the current status of this emerging field.

Investigation of protective effect of ethanol on the natural structure of protein with infrared spectroscopy

The stability of biological drugs with protein as an active substance depends heavily on the retention of natural protein structure during freeze-drying. Stabilizers have become important substances in the process of protein freeze-drying. In order to further understand the mechanism of the interaction between protein and stabilizers, human serum albumin (HSA) and simple hydroxyl compound ethanol were used as models. Infrared (IR) spectroscopy combined with chemometrics was implemented to investigate the changes of secondary structure and hydration of HSA when different concentrations of ethanol were considered as interference. Through the analysis of the protein secondary structure and hydrated layer, we found that the addition of ethanol-d6 increased the α-helix of HSA and reduced the disordered structure. The hydrogen bond structure around HSA was enhanced and intermolecular aggregation was reduced through the action of the water molecules. The hypothesis was verified by circular dichroism (CD) and transmission electron microscopy (TEM) observation by adding different concentrations of ethanol-d6. It was found that a small amount of ethanol could protect the native conformation of HSA. In conclusion, this study revealed the mechanism of ethanol as a protein protector, provided a new idea for protein purification process and a theoretical basis for biomolecular interaction.