Process analytical technology implementation for protein refolding: GCSF as a case study

Harnessing Liquid Crystal Sensors for High-Throughput Real-Time Detection of Structural Changes in Lysozyme during Refolding Processes

Despite the rapid advances in process analytical technology, the assessment of protein refolding efficiency has largely relied on off-line protein-specific assays and/or chromatographic procedures such as reversed-phase high-performance liquid chromatography and size exclusion chromatography. Due to the inherent time gap pertaining to traditional methods, exploring optimum refolding conditions for many recombinant proteins, often expressed as insoluble inclusion bodies, has proven challenging. The present study describes a novel protein refolding sensor that utilizes liquid crystals (LCs) to discriminate varying protein structures during unfolding and refolding. An LC layer containing 4-cyano-4'-pentylbiphenyl (5CB) intercalated with 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE) is used as a sensing platform, and its proof-of-concept performance is demonstrated using lysozyme as a model protein. As proteins unfold or refold, a local charge fluctuation at their surfaces modulates their interaction with zwitterionic phospholipid DOPE. This alters the alignment of DOPE molecules at the aqueous/LC interface, affecting the orientational ordering of bulk LC (i.e., homeotropic to planar for refolding and planar to homeotropic for unfolding). Differential polarized optical microscope images of the LC layer are subsequently generated, whose brightness directly linked to conformational changes of lysozyme molecules is quantified by gray scale analysis. Importantly, our LC-based refolding sensor is compatible with diverse refolding milieus for real-time analysis of lysozyme refolding and thus likely to facilitate the refolding studies of many proteins, especially those lacking a method to determine structure-dependent biological activity.

Artificial intelligence and machine learning applications in biopharmaceutical manufacturing

Artificial intelligence and machine learning (AI-ML) offer vast potential in optimal design, monitoring, and control of biopharmaceutical manufacturing. The driving forces for adoption of AI-ML techniques include the growing global demand for biotherapeutics and the shift toward Industry 4.0, spurring the rise of integrated process platforms and continuous processes that require intelligent, automated supervision. This review summarizes AI-ML applications in biopharmaceutical manufacturing, with a focus on the most used AI-ML algorithms, including multivariate data analysis, artificial neural networks, and reinforcement learning. Perspectives on the future growth of AI-ML applications in the area and the challenges of implementing these techniques at manufacturing scale are also presented.

Continuous integrated manufacturing for biopharmaceuticals: A new paradigm or an empty promise?

Continuous integrated bioprocessing has elicited considerable interest from the biopharma industry for the many purported benefits it promises. Today many major biopharma manufacturers around the world are engaged in the development of continuous process platforms for their products. In spite of great potential, the path toward continuous integrated bioprocessing remains unclear for the biologics industry due to legacy infrastructure, process integration challenges, vague regulatory guidelines, and a diverging focus toward novel therapies. In this article, we present a review and perspective on this topic. We explore the status of the implementation of continuous integrated bioprocessing among biopharmaceutical manufacturers. We also present some of the key hurdles that manufacturers are likely to face during this implementation. Finally, we hypothesize that the real impact of continuous manufacturing is likely to come when the cost of manufacturing is a substantial portion of the cost of product development, such as in the case of biosimilar manufacturing and emerging economies.

Refolding of Proteins Expressed as Inclusion Bodies in E. coli

Microbial-based biotherapeutics that are produced in Escherichia coli (E. coli) can be generated intracellularly in the form of inclusion bodies (IBs) or in soluble active form in periplasmic space or extracellularly. Overexpression of these biotherapeutics in E. coli leads to formation of insoluble aggregates called inclusion bodies. These IBs contain misfolded and inactive form of proteins which need to be refolded to obtain a functionally active form of proteins. Here, we discuss refolding of E. coli-based recombinant human granulocyte colony-stimulating factor (GCSF), expressed as IBs, and highlight some of the key features associated with the refolding kinetic reaction.

Refolding in the modern biopharmaceutical industry

Inclusion bodies (IBs) often emerge upon overexpression of recombinant proteins in E. coli. From IBs, refolding is necessary to generate the native protein that can be further purified to obtain pure and active biologicals. This work focusses on refolding as a significant process step during biopharmaceutical manufacturing with an industrial perspective. A theoretical and historical background on protein refolding gives the reader a starting point for further insights into industrial process development. Quality requirements on IBs as starting material for refolding are discussed and further economic and ecological aspects are considered with regards to buffer systems and refolding conditions. A process development roadmap shows the development of a refolding process starting from first exploratory screening rounds to scale-up and implementation in manufacturing plant. Different aspects, with a direct influence on yield, such as the selection of chemicals including pH, ionic strength, additives, etc., and other often neglected aspects, important during scale-up, such as mixing, and gas-fluid interaction, are highlighted with the use of a quality by design (QbD) approach. The benefits of simulation sciences (process simulation and computer fluid dynamics) and process analytical technology (PAT) for seamless process development are emphasized. The work concludes with an outlook on future applications of refolding and highlights open research inquiries.

Enablers of continuous processing of biotherapeutic products

The benefits of continuous processing over batch manufacturing are widely acknowledged across the biopharmaceutical industry, primary of which are higher productivity and greater consistency in product quality. Furthermore, the reduced equipment and facility footprint lead to significantly lower capital costs. Technology enablers have a major role in this migration from batch to continuous processing. In this review, we highlight the various enablers that are facilitating adoption of continuous upstream and downstream bioprocessing. This includes new bioreactors and cell retention devices for upstream operations, and on-column and continuous flow refolding, novel continuous chromatography, and single-pass filtration systems for downstream processes. We also elucidate the significant roles of process integration and control as well as of data analytics in these processes.

Advances in monitoring and control of refolding kinetics combining PAT and modeling

Overexpression of recombinant proteins in Escherichia coli results in misfolded and non-active protein aggregates in the cytoplasm, so-called inclusion bodies (IB). In recent years, a change in the mindset regarding IBs could be observed: IBs are no longer considered an unwanted waste product, but a valid alternative to produce a product with high yield, purity, and stability in short process times. However, solubilization of IBs and subsequent refolding is necessary to obtain a correctly folded and active product. This protein refolding process is a crucial downstream unit operation-commonly done as a dilution in batch or fed-batch mode. Drawbacks of the state-of-the-art include the following: the large volume of buffers and capacities of refolding tanks, issues with uniform mixing, challenging analytics at low protein concentrations, reaction kinetics in non-usable aggregates, and generally low re-folding yields. There is no generic platform procedure available and a lack of robust control strategies. The introduction of Quality by Design (QbD) is the method-of-choice to provide a controlled and reproducible refolding environment. However, reliable online monitoring techniques to describe the refolding kinetics in real-time are scarce. In our view, only monitoring and control of re-folding kinetics can ensure a productive, scalable, and versatile platform technology for re-folding processes. For this review, we screened the current literature for a combination of online process analytical technology (PAT) and modeling techniques to ensure a controlled refolding process. Based on our research, we propose an integrated approach based on the idea that all aspects that cannot be monitored directly are estimated via digital twins and used in real-time for process control. KEY POINTS: • Monitoring and a thorough understanding of refolding kinetics are essential for model-based control of refolding processes. • The introduction of Quality by Design combining Process Analytical Technology and modeling ensures a robust platform for inclusion body refolding.

Process analytical technology application for protein PEGylation using near infrared spectroscopy: G-CSF as a case study

Conjugation of protein therapeutics with polymers like polyethylene glycol (PEG) has been shown to increase their therapeutic efficiency. However, manufacturing of PEGylated drugs requires an additional, carefully controlled reaction step after purifying the protein, followed by further purification of over- and under-PEGylated variants. In this work, we have used a combined spectroscopic and statistical approach for monitoring and control of the PEGylation reaction for G-CSF using near infrared spectroscopy (NIRS). An online NIRS probe deployed in the reaction vessel has been used to track conversion of G-CSF into monoPEGylated and multiPEGylated forms using calibrated partial least squares regression models on the NIRS spectra which are collected in real time every 3 s. A pH probe integrated with a peristaltic pump facilitates automated quenching of the reaction at the targeted time. The NIRS spectra have also been used to build a batch evolution model for the reaction from end-to-end, including the addition of the reactants to the reaction vessel, the progress of the reaction for 70 min, and the final quenching with Tris base. Online spectra are compared against the statistical process control charts of the batch evolution model in real time to detect deviations as soon as they occur. The system was demonstrated for four common deviations in the PEGylation process, namely: delayed quenching time, wrong concentration of reducing agent added, wrong PEG to G-CSF ratio, and wrong sequence of addition of reactants. The system was able to identify all four deviations in real time and alert the operator to take control actions. The PAT approach suggested here embraces the quality by design framework and can be generalized for manufacturing scale monitoring and control of different biotechnology reactions with spectroscopic signatures.

Process Analytical Technologies and Data Analytics for the Manufacture of Monoclonal Antibodies

Process analytical technology (PAT) for the manufacture of monoclonal antibodies (mAbs) is defined by an integrated set of advanced and automated methods that analyze the compositions and biophysical properties of cell culture fluids, cell-free product streams, and biotherapeutic molecules that are ultimately formulated into concentrated products. In-line or near-line probes and systems are remarkably well developed, although challenges remain in the determination of the absence of viral loads, detecting microbial or mycoplasma contamination, and applying data-driven deep learning to process monitoring and soft sensors. In this review, we address the current status of PAT for both batch and continuous processing steps and discuss its potential impact on facilitating the continuous manufacture of biotherapeutics.

Automation of Dead End Filtration: An Enabler for Continuous Processing of Biotherapeutics

Dead end filtration is a critical unit operation that is used for primary and secondary clarification during manufacturing of both microbial and mammalian cell based biotherapeutics. Dead end filtration is conventionally done in batch mode and requires filter pre-sizing using extensive scouting studies, along with filter over-sizing before deployment to handle potential variability. However, continuous manufacturing processes require consistent use of dead-end filtration over weeks or months, with potential unpredictable variations in feed stream attributes, which is a challenge currently facing the industry. In this work, a dead-end filtration skid is designed for continuous depth filtration, incorporating multiple small-sized filters along with turbidity, and pressure sensors with immediate switching to a fresh filter whenever turbidity or pressure breakthrough above a pre-determined cut-off is detected in real time. The skid has been successfully tested for manufacturing of granulocyte colony stimulating factor from Escherichia coli, human serum albumin from Pichia pastoris, and a monoclonal antibody therapeutic from CHO cells. The proposed skid can be directly applied for any dead-end filtration application with minimal prior scouting studies or sizing calculations for scale-up. It is a useful solution for continuous processing trains where the nature of the feed, such as its turbidity or host cell proteins content, may change over long continuous campaigns, rendering previous sizing calculations inaccurate. The skid also allows significant cost savings by eliminating the sizing safety factor of 1.5-2x which is generally added before filter deployment at manufacturing scale.

The uniqueness of flow in probing the aggregation behavior of clinically relevant antibodies

The development of therapeutic monoclonal antibodies (mAbs) can be hindered by their tendency to aggregate throughout their lifetime, which can illicit immunogenic responses and render mAb manufacturing unfeasible. Consequently, there is a need to identify mAbs with desirable thermodynamic stability, solubility, and lack of self-association. These behaviors are assessed using an array of in silico and in vitro assays, as no single assay can predict aggregation and developability. We have developed an extensional and shear flow device (EFD), which subjects proteins to defined hydrodynamic forces which mimic those experienced in bioprocessing. Here, we utilize the EFD to explore the aggregation propensity of 33 IgG1 mAbs, whose variable domains are derived from clinical antibodies. Using submilligram quantities of material per replicate, wide-ranging EFD-induced aggregation (9-81% protein in pellet) was observed for these mAbs, highlighting the EFD as a sensitive method to assess aggregation propensity. By comparing the EFD-induced aggregation data to those obtained previously from 12 other biophysical assays, we show that the EFD provides distinct information compared with current measures of adverse biophysical behavior. Assessing a candidate's liability to hydrodynamic force thus adds novel insight into the rational selection of developable mAbs that complements other assays.

Process Analytical Technology Implementation for Peptide Manufacturing: Cleavage Reaction of Recombinant Lethal Toxin Neutralizing Factor Concatemer as a Case Study

The α-chymotrypsin-based cleavage reaction is necessary for manufacturing peptides using rDNA technology with tandem repeats. The current work showcases application of process analytical technology (PAT) tools for monitoring and control of this reaction, using recombinant Lethal Toxin Neutralizing Factor (rLTNF) as a case study. At-line Fourier Transform infrared spectroscopy (ATR-FTIR) combined with attenuated total internal reflectance sampling accessory was exploited to monitor the reaction. PLS spectral calibration models were created for real-time quantification of concentrations of rLTNF concatemer and urea in the reaction mixture. An end-to-end PAT monitoring and control strategy was developed to address potential deviations and ensure that targets for yield, purity, and impurity profile are met for each batch. The impact of various deviations of process parameters outside the operating space, such as deviations in the reaction buffer, concentration of concatemer in the IBs, enzyme loading relative to protein concentration, and reaction time with late quenching were investigated. Variation in impurity profile over time in the case of late reaction quenching was determined through HPLC and mass spectrometry. It has been demonstrated how process signatures from the PAT tools across various batches and campaigns can be analyzed to facilitate real-time process monitoring and control.

Recent Developments in Bioprocessing of Recombinant Proteins: Expression Hosts and Process Development

Infectious diseases, along with cancers, are among the main causes of death among humans worldwide. The production of therapeutic proteins for treating diseases at large scale for millions of individuals is one of the essential needs of mankind. Recent progress in the area of recombinant DNA technologies has paved the way to producing recombinant proteins that can be used as therapeutics, vaccines, and diagnostic reagents. Recombinant proteins for these applications are mainly produced using prokaryotic and eukaryotic expression host systems such as mammalian cells, bacteria, yeast, insect cells, and transgenic plants at laboratory scale as well as in large-scale settings. The development of efficient bioprocessing strategies is crucial for industrial production of recombinant proteins of therapeutic and prophylactic importance. Recently, advances have been made in the various areas of bioprocessing and are being utilized to develop effective processes for producing recombinant proteins. These include the use of high-throughput devices for effective bioprocess optimization and of disposable systems, continuous upstream processing, continuous chromatography, integrated continuous bioprocessing, Quality by Design, and process analytical technologies to achieve quality product with higher yield. This review summarizes recent developments in the bioprocessing of recombinant proteins, including in various expression systems, bioprocess development, and the upstream and downstream processing of recombinant proteins.