Comparison of predicted extinction coefficients of monoclonal antibodies with experimental values as measured by the Edelhoch method

TEMPRO: nanobody melting temperature estimation model using protein embeddings

Single-domain antibodies (sdAbs) or nanobodies have received widespread attention due to their small size (~ 15 kDa) and diverse applications in bio-derived therapeutics. As many modern biotechnology breakthroughs are applied to antibody engineering and design, nanobody thermostability or melting temperature (Tm) is crucial for their successful utilization. In this study, we present TEMPRO which is a predictive modeling approach for estimating the Tm of nanobodies using computational methods. Our methodology integrates various nanobody biophysical features to include Evolutionary Scale Modeling (ESM) embeddings, NetSurfP3 structural predictions, pLDDT scores per sdAb region from AlphaFold2, and each sequence's physicochemical characteristics. This approach is validated with our combined dataset containing 567 unique sequences with corresponding experimental Tm values from a manually curated internal data and a recently published nanobody database, NbThermo. Our results indicate the efficacy of protein embeddings in reliably predicting the Tm of sdAbs with mean absolute error (MAE) of 4.03 °C and root mean squared error (RMSE) of 5.66 °C, thus offering a valuable tool for the optimization of nanobodies for various biomedical and therapeutic applications. Moreover, we have validated the models' performance using experimentally determined Tms from nanobodies not found in NbThermo. This predictive model not only enhances nanobody thermostability prediction, but also provides a useful perspective of using embeddings as a tool for facilitating a broader applicability of downstream protein analyses.

Systematically amino acid analysis: Advancements in extinction coefficient determination for therapeutic proteins

Biologicals developers often face challenges in accurately determining the extinction coefficient (EC) measurement. We have successfully improved the precision and robustness of the widely recognized amino acid analysis method for EC determination, through a stepwise optimization process. Extensive analyses based on 114 observations, covering eight proteins over three years were performed, with a maximum relative standard deviation of 1.5% among multiple analysts, and a maximum deviation of 2.8% from the theoretical EC across the eight given proteins examined.

Subtractive Proteomics and Reverse-Vaccinology Approaches for Novel Drug Target Identification and Chimeric Vaccine Development against Bartonella henselae Strain Houston-1

Bartonella henselae is a Gram-negative bacterium causing a variety of clinical symptoms, ranging from cat-scratch disease to severe systemic infections, and it is primarily transmitted by infected fleas. Its status as an emerging zoonotic pathogen and its capacity to persist within host erythrocytes and endothelial cells emphasize its clinical significance. Despite progress in understanding its pathogenesis, limited knowledge exists about the virulence factors and regulatory mechanisms specific to the B. henselae strain Houston-1. Exploring these aspects is crucial for targeted therapeutic strategies against this versatile pathogen. Using reverse-vaccinology-based subtractive proteomics, this research aimed to identify the most antigenic proteins for formulating a multi-epitope vaccine against the B. henselae strain Houston-1. One crucial virulent and antigenic protein, the PAS domain-containing sensor histidine kinase protein, was identified. Subsequently, the identification of B-cell and T-cell epitopes for the specified protein was carried out and the evaluated epitopes were checked for their antigenicity, allergenicity, solubility, MHC binding capability, and toxicity. The filtered epitopes were merged using linkers and an adjuvant to create a multi-epitope vaccine construct. The structure was then refined, with 92.3% of amino acids falling within the allowed regions. Docking of the human receptor (TLR4) with the vaccine construct was performed and demonstrated a binding energy of -1047.2 Kcal/mol with more interactions. Molecular dynamic simulations confirmed the stability of this docked complex, emphasizing the conformation and interactions between the molecules. Further experimental validation is necessary to evaluate its effectiveness against B. henselae.

Quantification of SARS-CoV-2 monoclonal IgG mass fraction by isotope dilution mass spectrometry

The availability of serology assays to measure antibodies against the SARS coronavirus 2 (SARS-CoV-2) expanded rapidly during the Covid-19 pandemic. The interchangeable use of such assays to monitor disease progression and immune protection requires their standardization, for which suitably characterized monoclonal antibody materials can be useful. The methods, based on isotope dilution mass spectrometry, to value assign the mass fraction of such a material in solution within the context of an international interlaboratory comparison study (CCQM-P216) are described. The mass fraction in solution of a humanized IgG monoclonal antibody (mAb) against the SARS-CoV-2 Spike glycoprotein in the study sample has been value assigned through a combination of liquid chromatography, isotope dilution mass spectrometry (LC-ID-MS) methods and size exclusion chromatography with UV detection (SEC-UV). The former were developed for the quantification of amino acids and proteotypic peptides as surrogate analytes of the mAb while the latter was applied for the determination of the relative monomeric mass fraction. High-resolution mass spectrometry (hrMS) allowed the molecular weight evaluation and ruled out the presence of significant impurities. Method trueness was assessed using a subclass homologous IgG1 material value assigned by amino acid analysis. The assigned mass fraction of monomeric SARS-CoV-2 IgG in solution was 390 ± 16 mg/g. The associated expanded uncertainty originated mainly from acid hydrolysis variability and Trypsin/Lys-C digestion variability and efficiency.

Correcting Ultraviolet-Visible Spectra for Baseline Artifacts

Rayleigh and Mie light scattering from particulates, soluble protein aggregates, or large proteins can lead to inaccuracy of concentration measurements using ultraviolet (UV) spectroscopy and Beer's Law. While a number of light scattering correction equations have been proposed in the literature, they can also lead to incorrect values if samples vary in particulate and/or soluble aggregate levels or depart in other ways from which the equations were developed. We propose a curve-fitting baseline subtraction approach based on fundamental Rayleigh and Mie scattering equations which also factors in instrument baseline artifacts. We validated this Rayleigh-Mie correction against a wide variety of positive and negative controls, including protein size standards, protein aggregates induced by forced degradation, lentivirus and polystyrene nanospheres.

Optimal loading flow rate trajectory in monoclonal antibody capture chromatography

In this paper, we determined the optimal flow rate trajectory during the loading phase of a mAb capture column. For this purpose, a multi-objective function was used, consisting of productivity and resin utilization. Several general types of trajectories were considered, and the optimal Pareto points were obtained for all of them. In particular, the presented trajectories include a constant-flow loading process as a nominal approach, a stepwise trajectory, and a linear trajectory. Selected trajectories were then applied in experiments with the state-of-the-art protein A resin mAb Select PrismA^TM, running in batch mode on a standard single-column chromatography setup, and using both a purified mAb solution as well as a clarified supernatant. The results show that this simple approach, programming the volumetric flow rate according to either of the explored strategies, can improve the process economics by increasing productivity by up to 12% and resin utilization by up to 9% compared to a constant-flow process, while obtaining a yield higher than 99%. The productivity values were similar to the ones obtained in a multi-column continuous process, and ranged from 0.23 to 0.35 mg/min/mL resin. Additionally, it is shown that a model calibration carried out at constant flow can be applied in the simulation and optimization of flow trajectories. The selected processes were scaled up to pilot scale and simulated to prove that even higher productivity and resin utilization can be achieved at larger scales, and therefore confirm that the trajectories are generalizable across process scales for this resin.

Shortwave-infrared (SWIR) fluorescence molecular imaging using indocyanine green-antibody conjugates for the optical diagnostics of cancerous tumours

Recently, shortwave-infrared (SWIR, 1000-1400 nm) fluorescence imaging has attracted much attention due to the higher contrast and sensitivity with deeper penetration depths compared to conventional visible and near-infrared (NIR) fluorescence imaging. For the SWIR fluorescence imaging, the development of fluorescent probes emitting over 1000 nm is necessary. So far, a variety of SWIR fluorescent probes based on single-walled carbon nanotubes, quantum dots, rare-metal doped nanomaterials, and organic dyes have been developed. However, there are a very limited number of biocompatible SWIR fluorescent probes, which can be used to biomedical applications. Among NIR and SWIR fluorescent probes, indocyanine green (ICG) is the only fluorescent dye approved by US Food and Drug Administration (FDA) for clinical use. Although ICG has a fluorescence maximum at a NIR region (ca. 830 nm), ICG emits in the SWIR region over 1000 nm. Here, we present ICG-based SWIR fluorescence molecular imaging for the highly-sensitive optical detection of breast and skin tumours in mice. As SWIR fluorescent molecular-imaging probes, we synthesized ICG-antibody conjugates, which prepared from anti-HER2 antibody (Herceptin), anti-EGFR antibody (Erbitux), anti-VEGFR-2 antibody (Cyramza), and anti-PD-L1 antibody (anti-PD-L1 ab). The present SWIR molecular imaging probes specifically accumulated to the breast and skin tumours, and their SWIR fluorescence images (>1000 nm) showed 1.5-2.0 times higher contrast than NIR tumour images taken at 830 nm. We show that the SWIR fluorescence imaging using ICG-antibody conjugates can be used for the elucidation of expression level of cancer-specific membrane proteins, HER2, EGFR, VEGFR-2, and PD-L1 in vivo. We also show that the SWIR fluorescence imaging enables quantitative analysis of the change in the size of tumour treated with an anti-cancer drug, Kadcyla. Our findings suggest that the SWIR fluorescence molecular imaging using ICG-antibody conjugates has potential to use for the optical diagnostics of cancerous tumors in medical and clinical fields.

The NISTmAb Reference Material 8671 value assignment, homogeneity, and stability

The NISTmAb Reference Material (RM) 8671 is intended to be an industry standard monoclonal antibody for pre-competitive harmonization of best practices and designing next generation characterization technologies for identity, quality, and stability testing. It must therefore embody the quality and characteristics of a typical biopharmaceutical product and be available long-term in a stable format with consistent product quality attributes. A stratified sampling and analysis plan using a series of qualified analytical and biophysical methods is described that assures RM 8671 meets these criteria. Results for the first three lots of RM 8671 highlight the consistency of material attributes with respect to size, charge, and identity. RM 8671 was verified to be homogeneous both within and between vialing lots, demonstrating the robustness of the lifecycle management plan. It was analyzed in concert with the in-house primary sample 8670 (PS 8670) to provide a historical link to this seminal material. RM 8671 was verified to be fit for its intended purpose as a technology innovation tool, external system suitability control, and cross-industry harmonization platform. Graphical abstract The NISTmAb Reference Material (RM) 8671 is intended to be an industry standard monoclonal antibody for pre-competitive harmonization of best practices and designing next generation characterization technologies for identity, quality, and stability testing.

Rediscovery and Revival of Analytical Refractometry for Protein Determination: Recombining Simplicity With Accuracy in the Digital Era

Among "vintage" methods of protein determination, quantitative analytical refractometry has received far less attention than well-established pharmacopoeial techniques based on protein nitrogen content, such as Dumas combustion (1831) and Kjeldahl digestion (1883). Protein determination by quantitative refractometry dates back to 1903 and has been extensively investigated and characterized in the following 30 years, but has since vanished into a few niche applications that may not require the degree of accuracy and precision essential for pharmaceutical analysis. However, because high-resolution and precision digital refractometers have replaced manual instruments, reducing time and resource consumption, the method appears particularly attractive from an economic, ergonomic, and environmental viewpoint. The sample solution can be measured without dilution or other preparation procedures than the separation of the protein-free matrix by ultrafiltration, which might even be omitted for a constant matrix and excipient composition.