Preferential interactions between protein and arginine: Effects of arginine on tertiary conformational and colloidal stability of protein solution

ConoGPT: Fine-Tuning a Protein Language Model by Incorporating Disulfide Bond Information for Conotoxin Sequence Generation

Conotoxins are a class of peptide toxins secreted by marine mollusks of the Conus genus, characterized by their unique mechanism of action and significant biological activity, making them highly valuable for drug development. However, traditional methods of acquiring conotoxins, such as in vivo extraction or chemical synthesis, face challenges of high costs, long cycles, and limited exploration of sequence diversity. To address these issues, we propose the ConoGPT model, a conotoxin sequence generation model that fine-tunes the ProtGPT2 model by incorporating disulfide bond information. Experimental results demonstrate that sequences generated by ConoGPT exhibit high consistency with authentic conotoxins in physicochemical properties and show considerable potential for generating novel conotoxins. Furthermore, compared to models without disulfide bond information, ConoGPT outperforms in terms of generating sequences with ordered structures. The majority of the filtered sequences were shown to possess significant binding affinities to nicotinic acetylcholine receptor (nAChR) targets based on molecular docking. Molecular dynamics simulations of the selected sequences further confirmed the dynamic stability of the generated sequences in complex with their respective targets. This study not only provides a new technological approach for conotoxin design but also offers a novel strategy for generating functional peptides.

Explainable Machine Learning Models to Predict Gibbs-Donnan Effect During Ultrafiltration and Diafiltration of High-Concentration Monoclonal Antibody Formulations

Evaluating the Gibbs-Donnan and volume exclusion effects during protein ultrafiltration and diafiltration (UF/DF) is crucial in biopharmaceutical process development to precisely control the concentration of the drug substance in the final formulation. Understanding the interactions between formulation excipients and proteins under these conditions requires a domain-specific knowledge of molecular-level phenomena. This study developed gradient boosted tree models to predict the Gibbs-Donnan and volume exclusion effects for amino acids and therapeutic monoclonal antibodies using simple molecular descriptors. The models' predictions were interpreted by information gain and Shapley additive explanation (SHAP) values to understand the modes of action of the antibodies and excipients and to validate the models. The results translated feature effects in machine learning to real-world molecular interactions, which were cross-referenced with existing scientific literature for verification. The models were validated in pilot-scale manufacturing runs of two antibody products requiring high levels of concentration. By only requiring a molecule's biophysicochemical descriptors and process conditions, the proposed models provide an in silico alternative to conventional UF/DF experiments to accelerate process development and boost process understanding of the underlying molecular mechanisms through rational interpretation of the models.

Stability of Protein Pharmaceuticals: Recent Advances

There have been significant advances in the formulation and stabilization of proteins in the liquid state over the past years since our previous review. Our mechanistic understanding of protein-excipient interactions has increased, allowing one to develop formulations in a more rational fashion. The field has moved towards more complex and challenging formulations, such as high concentration formulations to allow for subcutaneous administration and co-formulation. While much of the published work has focused on mAbs, the principles appear to apply to any therapeutic protein, although mAbs clearly have some distinctive features. In this review, we first discuss chemical degradation reactions. This is followed by a section on physical instability issues. Then, more specific topics are addressed: instability induced by interactions with interfaces, predictive methods for physical stability and interplay between chemical and physical instability. The final parts are devoted to discussions how all the above impacts (co-)formulation strategies, in particular for high protein concentration solutions.'

Effects of arginine in therapeutic protein formulations: a decade review and perspectives

Arginine (Arg) is a natural amino acid with an acceptable safety profile and a unique chemical structure. Arg and its salts are highly effective in enhancing protein refolding and solubilization, suppressing protein-protein interaction and aggregation and reducing viscosity of high concentration protein formulations. Arg and its salts have been used in research and 20 approved protein injectables. This review summarizes the effects of Arg as an excipient in therapeutic protein formulations with the focus on its physicochemical properties, safety, applications in approved protein products, beneficial and detrimental effects in liquid and lyophilized protein formulations when combined with different counterions and mechanism on protein stabilization and destabilization. The decade literature review indicates that the benefits of Arg overweigh its risks when it is used appropriately. It is recommended to add Arg along with glutamate as a counterion to high concentration protein formulations on top of sugars or polyols to counterbalance the negative effects of Arg hydrochloride. The use of Arg as a viscosity reducer and protein stabilizer in high concentration formulations will be the inevitable future trend of the biopharmaceutical industry for subcutaneous administration.

An Intercompany Perspective on Practical Experiences of Predicting, Optimizing and Analyzing High Concentration Biologic Therapeutic Formulations

Developing high-dose biologic drugs for subcutaneous injection often requires high-concentration formulations and optimizing viscosity, solubility, and stability while overcoming analytical, manufacturing, and administration challenges. To understand industry approaches for developing high-concentration formulations, the Formulation Workstream of the BioPhorum Development Group, an industry-wide consortium, conducted an inter-company collaborative exercise which included several surveys. This collaboration provided an industry perspective, experience, and insight into the practicalities for developing high-concentration biologics. To understand solubility and viscosity, companies desire predictive tools, but experience indicates that these are not reliable and experimental strategies are best. Similarly, most companies prefer accelerated and stress stability studies to in-silico or biophysical-based prediction methods to assess aggregation. In addition, optimization of primary container-closure and devices are pursued to mitigate challenges associated with high viscosity of the formulation. Formulation strategies including excipient selection and application of studies at low concentration to high-concentration formulations are reported. Finally, analytical approaches to high concentration formulations are presented. The survey suggests that although prediction of viscosity, solubility, and long-term stability is desirable, the outcome can be inconsistent and molecule dependent. Significant experimental studies are required to confirm robust product definition as modeling at low protein concentrations will not necessarily extrapolate to high concentration formulations.

N-Acetylated-L-arginine (NALA) is an enhanced protein aggregation suppressor under interfacial stresses and elevated temperature for protein liquid formulations

Even though arginine hydrochloride has been recognized as a protein aggregation suppressor in the biopharmaceutical industry, its use has been questioned due to decreasing transition unfolding temperatures (T_m). Four compounds were designed to enhance the role of arginine by changing the length of the carbon chain with removal or N-acetylation of α-amino group. Biophysical properties were observed by differential scanning calorimetry (DSC), dynamic light scattering (DLS), size-exclusion chromatography (SEC), and flow imaging (FI). N-Acetyl-L-arginine (NALA) performed the best at minimizing decrease in T_m with arginine at different pH. NALA also demonstrated relatively higher colloidal stability than arginine hydrochloride, especially in the acidic pH, thereby reducing agitation stress of IgG. Moreover, NALA exhibited a cooperative effect with commercially used glycine buffer for IVIG to maintain the monomer contents with almost no change and suppressed larger particle formation after agitation with heat. The study concludes that the decreasing T_m of proteins by arginine hydrochloride is due to amide group in the α-carbon chain. Moreover, chemical modification on the group compared to removing it will be a breakthrough of arginine's limitations and optimize storage stability of protein therapeutics.

Al (III) metal augment thermal aggregation and fibrillation in protein: Role of metal toxicity in neurological diseases

Protein fibrillation is a leading cause of innumerable neurodegenerative diseases. The exact underlying mechanism associated with the formation of fibrils is yet to be known. Recently, the role of metal ions resulting into fibrillation of proteins has gained attention of the scientific community. In this piece of work, we have investigated the effect of the aluminum (Al) metal ion on the kinetics of aggregation of bovine serum albumin (BSA) protein under physiological conditions by employing several biophysical and microscopic techniques. Quenching of tryptophan fluorescence was observed along with 9 nm blue shift, demonstrating BSA becomes more hydrophobic during unfolding pathway of thermal denaturation. Moreover, ANS (8-Anilino-1-naphthalene sulfonic acid) binding shows quenching in fluorescence intensity with increasing time of incubation at 65 °C, suggesting unfolding leading to the disruption of hydrophobic patches in BSA. Besides, Thioflavin T intensity indicated a significant acceleration in BSA fibrillation at a ratio of 1:1 and 1:2 of BSA and Al (III) metal ion respectively. In addition, circular dichroism (CD) spectroscopy study revealed the transition of BSA from α-helical conformation to the β-sheet rich structure. Molecular docking analysis demonstrated significant binding affinity (-1.2 kcal/mol) of Al (III) with BSA involving Phe501, Phe506, Val575, Thr578, Gln579, Leu531 residues. Transmission electron microscopy (TEM) reaffirm augmentation of thermal-induced BSA fibril formation in the presence of Al (III) metal ions. This study highlights the metal chelating potency as the possible therapeutic target for neurological diseases.

Damage of proteins at the air/water interface: Surface tension characterizes globulin interface stability

In the present study, we aimed to see what circumstances may cause protein damage at air/water interface and reveal the correlation between the surface properties of protein solution and the interface stability. The surface hydrophobicity and β-sheet of protein were determined by exogenous fluorescent probes, and the changes in the spatial structure of proteins were characterized by steady-state fluorescence spectroscopy. The surface tension was determined by the plate method, and such value was used to establish the correlation with the hydrophobicity and structure of the protein. Moreover, degree of aggregation in the presence or absence of Hofmeister salt in protein solution was investigated. There was a significant correlation between the surface tension and hydrophobicity of the protein solution (P < 0.05). The surface tension and structure of the protein also showed a significant correlation under the induction of pH (P < 0.05). Furthermore, when the protein was induced by the air/water interface, the surface tension, hydrophobicity, and structure of proteins were correlated, and protein aggregation was increased. When the additive induced a decrease in the surface tension of the protein solution, the protein aggregation was promoted. These findings provided valuable insights into the relationship between surface tension of the protein solution and interfacial stability and paved the way for future pre-formulation studies of therapeutic proteins.

Inhibition effect of thiol-type antioxidants on protein oxidative aggregation caused by free radicals

This study was aimed to investigate the inhibition effect of thiol-type antioxidants on protein oxidative aggregation caused by free radicals and the underlying mechanisms using six different thiol-type antioxidants (N-acetyl-L-cysteine, methionine, taurine, alpha-lipoic acid, glutathione and thioproline), Cu²⁺-H₂O₂ as a free radical generator (mainly a hydroxyl radical generator) and bovine serum albumin as the model protein. The inhibition effect of these antioxidants on protein oxidative aggregation and protective effect against oxidative damage in mouse brain tissues were investigated using SDS-PAGE, intrinsic fluorescence, simultaneous fluorescence, thioflavin T fluorescence, Congo red absorbance and inverted microscope. The results showed that all six antioxidants could inhibit protein oxidative aggregation by scavenging free radicals. In addition, alpha-lipoic acid could also bind to proteins via hydrophobic interactions and thioproline could bind to proteins via hydrogen bonds and van der Waals forces, thereby showing much stronger inhibition effect than others. Moreover, alpha-lipoic acid and thioproline could effectively prevent oxidative damage of mouse brain tissues. These results suggest that alpha-lipoic acid and thioproline can effectively inhibit free radical-induced protein aggregation and brain damage, which are worth testing for further anti-Alzheimer properties.

Dipicolinic acid as a novel spore-inspired excipient for antibody formulation

Ionic excipients are commonly used in aqueous therapeutic monoclonal antibody (mAb) formulations. Novel excipients are of industrial interest, with a recent focus on Arg salt forms and their application as viscosity reducing and stabilizing additives. Here, we report that the calcium salt of dipicolinic acid (DPA, pyridine-2,6-dicarboxylic acid), uniquely present in nature in the core of certain bacterial spores, reduces the viscosity of a mAb formulated at 150mg/mL, below that achieved by Arg hydrochloride at the same concentration (10mM). DPA also reduced the reversible phase separation of the same formulation, which characteristically occurs for this mAb upon cooling to 4°C. Differential scanning calorimetry and differential scanning fluorimetry did not reveal a conformation destabilisation of the mAb in the presence of 10mM DPA, or by the related quinolinic acid (QA, pyridine-2,3-dicarboxylic acid). However, fluorescence spectrophotometry did reveal localised (aromatic) conformational changes to the mAb attributed to DPA, dependent on the salt form. While precise mechanisms of action remain to be identified, our preliminary data suggest that these DPA salts are worthy of further investigation as novel ionic excipient for biologics formulation.

Kinetics of Thermal Denaturation and Aggregation of Bovine Serum Albumin

Thermal aggregation of bovine serum albumin (BSA) has been studied using dynamic light scattering, asymmetric flow field-flow fractionation and analytical ultracentrifugation. The studies were carried out at fixed temperatures (60°C, 65°C, 70°C and 80°C) in 0.1 M phosphate buffer, pH 7.0, at BSA concentration of 1 mg/ml. Thermal denaturation of the protein was studied by differential scanning calorimetry. Analysis of the experimental data shows that at 65°C the stage of protein unfolding and individual stages of protein aggregation are markedly separated in time. This circumstance allowed us to propose the following mechanism of thermal aggregation of BSA. Protein unfolding results in the formation of two forms of the non-native protein with different propensity to aggregation. One of the forms (highly reactive unfolded form, U_hr) is characterized by a high rate of aggregation. Aggregation of U_hr leads to the formation of primary aggregates with the hydrodynamic radius (R_h,1) of 10.3 nm. The second form (low reactive unfolded form, U_lr) participates in the aggregation process by its attachment to the primary aggregates produced by the U_hr form and possesses ability for self-aggregation with formation of stable small-sized aggregates (A_st). At complete exhaustion of U_lr, secondary aggregates with the hydrodynamic radius (R_h,2) of 12.8 nm are formed. At 60°C the rates of unfolding and aggregation are commensurate, at 70°C the rates of formation of the primary and secondary aggregates are commensurate, at 80°C the registration of the initial stages of aggregation is complicated by formation of large-sized aggregates.