Hybrid Models for the simulation and prediction of chromatographic processes for protein capture

Model-based optimization strategy for intensification in the chromatographic purification of oligonucleotides

Oligonucleotides (ONs) are acquiring clinical relevance and their demand is expected to grow. However, the ON production capacity is currently limited by high manufacturing costs. Since the purification of the target ON sequence from molecularly similar variants represents a major bottleneck, this work presents a resource-effective strategy for the optimization of their preparative reversed-phase chromatographic purification. First, a model based on the equilibrium-dispersive theory was introduced to describe the chromatographic operation. Considering a deoxyribose nucleic acid with 20 nucleobases as case study, a genetic algorithm was developed to efficiently determine the adsorption isotherm and mass transfer parameters for the target ON and impurities. After the estimation of these parameters, a strategy for the in-silico optimization of the operation was established. The product collection window, gradient duration, and resin loading were considered as process variables and their influence on yield and productivity was investigated after setting a purity specification of 99.0%. The optimal process parameters identified through this analysis were experimentally verified, confirming the reliability of the model, calibrated with only 5 experimental runs. In addition, this optimal setpoint was exploited to design the multicolumn countercurrent solvent gradient purification (MCSGP) of this ON mixture, which allowed to boost the yield of the process and to work at cyclic steady state, while respecting the purity constraint. This study confirmed the potential of this in-silico optimization strategy in both improving the performance of the traditional single-column operations and in the rapid development of multicolumn processes.

Using artificial neural networks to accelerate flowsheet optimization for downstream process development

An optimal purification process for biopharmaceutical products is important to meet strict safety regulations, and for economic benefits. To find the global optimum, it is desirable to screen the overall design space. Advanced model-based approaches enable to screen a broad range of the design-space, in contrast to traditional statistical or heuristic-based approaches. Though, chromatographic mechanistic modeling (MM), one of the advanced model-based approaches, can be speed-limiting for flowsheet optimization, which evaluates every purification possibility (e.g., type and order of purification techniques, and their operating conditions). Therefore, we propose to use artificial neural networks (ANNs) during global optimization to select the most optimal flowsheets. So, the number of flowsheets for final local optimization is reduced and consequently the overall optimization time. Employing ANNs during global optimization proved to reduce the number of flowsheets from 15 to only 3. From these three, one flowsheet was optimized locally and similar final results were found when using the global outcome of either the ANN or MM as starting condition. Moreover, the overall flowsheet optimization time was reduced by 50% when using ANNs during global optimization. This approach accelerates the early purification process design; moreover, it is generic, flexible, and regardless of sample material's type.

Sensors and chemometrics in downstream processing

The biopharmaceutical industry is still running in batch mode, mostly because it is highly regulated. In the past, sensors were not readily available and in-process control was mainly executed offline. The most important product parameters are quantity, purity, and potency, in addition to adventitious agents and bioburden. New concepts using disposable single-use technologies and integrated bioprocessing for manufacturing will dominate the future of bioprocessing. To ensure the quality of pharmaceuticals, initiatives such as Process Analytical Technologies, Quality by Design, and Continuous Integrated Manufacturing have been established. The aim is that these initiatives, together with technology development, will pave the way for process automation and autonomous bioprocessing without any human intervention. Then, real-time release would be realized, leading to a highly predictive and robust biomanufacturing system. The steps toward such automated and autonomous bioprocessing are reviewed in the context of monitoring and control. It is possible to integrate real-time monitoring gradually, and it should be considered from a soft sensor perspective. This concept has already been successfully implemented in other industries and requires relatively simple model training and the use of established statistical tools, such as multivariate statistics or neural networks. This review describes a scenario for integrating soft sensors and predictive chemometrics into modern process control. This is exemplified by selective downstream processing steps, such as chromatography and membrane filtration, the most common unit operations for separation of biopharmaceuticals.

Building blocks needed for mechanistic modeling of bioprocesses: A critical review based on protein production by CHO cells

This paper reviews the key building blocks needed to develop a mechanistic model for use as an operational production tool. The Chinese Hamster Ovary (CHO) cell, one of the most widely used hosts for antibody production in the pharmaceutical industry, is considered as a case study. CHO cell metabolism is characterized by two main phases, exponential growth followed by a stationary phase with strong protein production. This process presents an appropriate degree of complexity to outline the modeling strategy. The paper is organized into four main steps: (1) CHO systems and data collection; (2) metabolic analysis; (3) formulation of the mathematical model; and finally, (4) numerical solution, calibration, and validation. The overall approach can build a predictive model of target variables. According to the literature, one of the main current modeling challenges lies in understanding and predicting the spontaneous metabolic shift. Possible candidates for the trigger of the metabolic shift include the concentration of lactate and carbon dioxide. In our opinion, ammonium, which is also an inhibiting product, should be further investigated. Finally, the expected progress in the emerging field of hybrid modeling, which combines the best of mechanistic modeling and machine learning, is presented as a fascinating breakthrough. Note that the modeling strategy discussed here is a general framework that can be applied to any bioprocess.

Realization of digital twin for dynamic control toward sample variation of ion exchange chromatography in antibody separation

Digital twin (DT) is a virtual and digital representation of physical objects or processes. In this paper, this concept is applied to dynamic control of the collection window in the ion exchange chromatography (IEC) toward sample variations. A possible structure of a feedforward model-based control DT system was proposed. Initially, a precise IEC mechanistic model was established through experiments, model fitting, and validation. The average root mean square error (RMSE) of fitting and validation was 8.1% and 7.4%, respectively. Then a model-based gradient optimization was performed, resulting in a 70.0% yield with a remarkable 11.2% increase. Subsequently, the DT was established by systematically integrating the model, chromatography system, online high-performance liquid chromatography, and a server computer. The DT was validated under varying load conditions. The results demonstrated that the DT could offer an accurate control with acidic variants proportion and yield difference of less than 2% compared to the offline analysis. The embedding mechanistic model also showed a positive predictive performance with an average RMSE of 11.7% during the DT test under >10% sample variation. Practical scenario tests indicated that tightening the control target could further enhance the DT robustness, achieving over 98% success rate with an average yield of 72.7%. The results demonstrated that the constructed DT could accurately mimic real-world situations and perform an automated and flexible pooling in IEC. Additionally, a detailed methodology for applying DT was summarized.

Sequential purification of cannabidiol by two-dimensional liquid chromatography combined with modeling and simulation of elution profiles

Cannabidiol (CBD) has garnered significant attention for its neuroprotective properties, and research on its therapeutic effects has increased dramatically in recent years. However, the systematic purification of CBD through scalable processes has remained bottleneck due to the structural similarities of the cannabinoids. Although preparative chromatography is considered as a potential solution, it is usually time-consuming and expensive. Therefore, the development of scalable strategy via fast and accurate optimization approach is crucial. The present study aimed to develop a sequential process for the scalable purification of CBD through an eco-friendly ethanolic extraction using ultrasonic assisted extraction, decarboxylation of cannabidiolic acid optimized by response surface methodology, followed by the development of off-line two-dimensional semi-preparative chromatography, boosted with stacked injection overloading. In the first dimension, a column packed with macroporous resin allows to enrich the target substance and then, the behavior of resin column for scale-up procedure were predicted and optimized by developed mathematical model. A C18 column was used in the second dimension. The CBD purity and recovery obtained were 94.3 and 82.1 %, respectively. A robust and reliable method was employed for CBD enrichment/purification, which can be generalized to other bioactive compounds in complex matrices.

Factors affecting therapeutic protein purity and yield during chromatographic purification

Therapeutic proteins are recombinant proteins generated through recombinant DNA technology and have attracted a great deal of interest in numerous applications, including pharmaceutical, cosmetic, human and animal health, agriculture, food, and bioremediation. Producing therapeutic proteins on a large scale, mainly in the pharmaceutical industry, necessitates a cost-effective, straightforward, and adequate manufacturing process. In industry, a protein separation technique based mainly on protein characteristics and modes of chromatography will be applied to optimize the purification process. Typically, the downstream process of biopharmaceutical operations may involve multiple chromatography phases that require the use of large columns pre-packed with resins that must be inspected before use. Approximately 20% of the proteins are assumed to be lost at each purification stage during the production of biotherapeutic products. Hence, to produce a high quality product, particularly in the pharmaceutical industry, the correct approach and understanding of the factors influencing purity and yield during purification are necessary.

Predictive mechanistic modeling of loading and elution in protein A chromatography

Protein A chromatography is an enabling technology in current manufacturing processes of monoclonal antibodies (mAbs) and mAb derivatives, largely due to its ability to reduce the levels of process-related impurities by several orders of magnitude. Despite its widespread application, the use of mathematical modeling capable of accurately predicting the full protein A chromatographic process, including loading, post-loading wash and elution stages, has been limited. This work describes a mechanistic modeling approach utilizing the general rate model (GRM), the capabilities of which are explored and optimized using two isotherm models. Isotherm parameters were estimated by inverse-fitting simulated breakthrough curves to experimental data at various pH values. The parameter values so obtained were interpolated across the relevant pH range using a best-fit curve, thus enabling their use in predictive modeling, including of elution over a range of pH. The model provides accurate predictions (< 3% mean error in 10% dynamic binding capacity predictions and ∼ 5% mean error in elution mass and pool volume predictions, both on scale-up) for various residence times, buffer conditions and elution schemes and its effectiveness for use in scale-up and process development is shown by applying the same parameters to larger columns and a wider range of residence times.

Current challenges and recent advances on the path towards continuous biomanufacturing

Continuous biopharmaceutical manufacturing is currently a field of intense research due to its potential to make the entire production process more optimal for the modern, ever-evolving biopharmaceutical market. Compared to traditional batch manufacturing, continuous bioprocessing is more efficient, adjustable, and sustainable and has reduced capital costs. However, despite its clear advantages, continuous bioprocessing is yet to be widely adopted in commercial manufacturing. This article provides an overview of the technological roadblocks for extensive adoptions and points out the recent advances that could help overcome them. In total, three key areas for improvement are identified: Quality by Design (QbD) implementation, integration of upstream and downstream technologies, and data and knowledge management. First, the challenges to QbD implementation are explored. Specifically, process control, process analytical technology (PAT), critical process parameter (CPP) identification, and mathematical models for bioprocess control and design are recognized as crucial for successful QbD realizations. Next, the difficulties of end-to-end process integration are examined, with a particular emphasis on downstream processing. Finally, the problem of data and knowledge management and its potential solutions are outlined where ontologies and data standards are pointed out as key drivers of progress.

Model-assisted process development, characterization and design of continuous chromatography for antibody separation

Continuous manufacturing in monoclonal antibody production has generated increased interest due to its consistent quality, high productivity, high equipment utilization, and low cost. One of the major challenges in realizing continuous biological manufacturing lies in implementing continuous chromatography. Given the complex operation mode and various operation parameters, it is challenging to develop a continuous process. Due to the process parameters being mainly determined by the breakthrough curves and elution behaviors, chromatographic modeling has gradually been used to assist in process development and characterization. Model-assisted approaches could realize multi-parameter interaction investigation and multi-objective optimization by integrating continuous process models. These approaches could reduce time and resource consumption while achieving a comprehensive and systematic understanding of the process. This paper reviews the application of modeling tools in continuous chromatography process development, characterization and design. Model-assisted process development approaches for continuous capture and polishing steps are introduced and summarized. The challenges and potential of model-assisted process characterization are discussed, emphasizing the need for further research on the design space determination strategy and parameter robustness analysis method. Additionally, some model applications for process design were highlighted to promote the establishment of the process optimization and process simulation platform.

Hybrid model development for parameter estimation and process optimization of hydrophobic interaction chromatography

Hydrophobic Interaction Chromatography (HIC) is often employed as a polishing step to remove aggregates for the purification of therapeutic proteins in the biopharmaceutical industry. To accelerate the process development and save the costs of performing time- and resource-intensive experiments, advanced model-based process design and optimization are necessary. Due to the unclear adsorption mechanism of the salt-dependent interaction between the protein and resin, the development of an accurate mechanistic model to describe the complex HIC behavior is challenging. In this work, an isotherm derived from Wang et al. is modified by adding three extra parameters together with an equilibrium dispersive model to represent the HIC process. To reduce the development effort of isotherm equations and extract missing information from the available data, a hybrid model is constructed by combining a simple and well-known multi-component Langmuir isotherm (MCL) with a neural network (NN). It is observed that the structure of the hybrid model is of critical importance to the accuracy of the developed model. During parameter estimation, a regularization strategy is incorporated to prevent overfitting. Furthermore, the impact of NN structures and regularization rates are comprehensively investigated. One of the interesting findings was that a simple NN with one hidden layer with two nodes and sigmoid as the activation function, significantly outperforms the mechanistic model, with a 62% improvement in accuracy in calibration and 31.4% in validation. To ensure the generalizability of the developed hybrid model, an in-silico dataset is generated using the mechanistic model to test the extrapolation capability of the hybrid model. Process optimization is also carried out to find the optimal operating conditions under product quality constraints using the developed hybrid model.

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.

Comparison of mechanistic and hybrid modeling approaches for characterization of a CHO cultivation process: Requirements, pitfalls and solution paths

Despite the advantages of mathematical bioprocess modeling, successful model implementation already starts with experimental planning and accordingly can fail at this early stage. For this study, two different modeling approaches (mechanistic and hybrid) based on a four-dimensional antibody-producing CHO fed-batch process are compared. Overall, 33 experiments are performed in the fractional factorial four-dimensional design space and separated into four different complex data partitions subsequently used for model comparison and evaluation. The mechanistic model demonstrates the advantage of prior knowledge (i.e., known equations) to get informative value relatively independently of the utilized data partition. The hybrid approach displayes a higher data dependency but simultaneously yielded a higher accuracy on all data partitions. Furthermore, our results demonstrate that independent of the chosen modeling framework, a smart selection of only four initial experiments can already yield a very good representation of a full design space independent of the chosen modeling structure. Academic and industry researchers are recommended to pay more attention to experimental planning to maximize the process understanding obtained from mathematical modeling.

Improving extracellular vesicles production through a Bayesian optimization-based experimental design

With the growing demand and diversity of biological drugs, developing optimal processes for their accelerated production with minimal resource utilization is a pressing challenge. Typically, such optimization involves multiple target properties, such as production yield, biological activity, and product purity. Therefore, strategic experimental design techniques that can characterize the parameter space while simultaneously arriving at the optimal process satisfying multiple target properties are required. To achieve this, we propose the use of a multi-objective batch Bayesian optimization (MOBBO) algorithm and illustrate its successful application for the production of extracellular vesicles (EVs) from a 3D culture of mesenchymal stem cells (MSCs) considering three objectives, namely to maximize the vesicle-to-protein ratio, maximize the enzymatic activity of the MSC-EV protein CD73, and minimize the amount of calregulin impurities. We show that the optimal combination of the process parameters to address the intended objectives could be achieved with only 32 experiments. For the four parameters considered (i.e., microcarrier concentration, seeding density, centrifugation time, and impeller speed), this number of experiments is comparable to or lower than the classical design of experiments (DoE) and the traditional one-factor-at-a-time (OFAT) approach. We illustrate how the algorithm adaptively samples in the process parameter space, selectively excluding unfavorable regions, thus minimizing the number of experiments required to reach optimal conditions. Finally, we compare the obtained solutions to the literature data and present possible applications of the collected data for other modeling activities such as Quality by Design, process monitoring, control, and scale-up.

Mathematical modeling and process analytical technology for continuous chromatography of biopharmaceutical products

Chromatography is a widely used separation method that is inherently a batch operation. However, the demand for higher productivity and lower cost and labor has prompted industries such as the petrochemical and food industries to transition from batch to continuous chromatography. Growing market competition in the biopharmaceutical industry and the rise of novel biotherapeutics modalities have brought about promising continuous chromatography methods as well as next-generation tools to enable continuous operation in bioprocessing. While these continuous chromatography methods outperform their batch counterpart, their implementation presents challenges due to their greater complexity. This review discusses two key technologies that are essential for the implementation of continuous chromatography: mathematical modeling and novel process analytical technologies. Mechanistic-based models not only aid in process development and optimization but also allow for greater process control and automation.

The use of predictive models to develop chromatography-based purification processes

Chromatography is the workhorse of biopharmaceutical downstream processing because it can selectively enrich a target product while removing impurities from complex feed streams. This is achieved by exploiting differences in molecular properties, such as size, charge and hydrophobicity (alone or in different combinations). Accordingly, many parameters must be tested during process development in order to maximize product purity and recovery, including resin and ligand types, conductivity, pH, gradient profiles, and the sequence of separation operations. The number of possible experimental conditions quickly becomes unmanageable. Although the range of suitable conditions can be narrowed based on experience, the time and cost of the work remain high even when using high-throughput laboratory automation. In contrast, chromatography modeling using inexpensive, parallelized computer hardware can provide expert knowledge, predicting conditions that achieve high purity and efficient recovery. The prediction of suitable conditions in silico reduces the number of empirical tests required and provides in-depth process understanding, which is recommended by regulatory authorities. In this article, we discuss the benefits and specific challenges of chromatography modeling. We describe the experimental characterization of chromatography devices and settings prior to modeling, such as the determination of column porosity. We also consider the challenges that must be overcome when models are set up and calibrated, including the cross-validation and verification of data-driven and hybrid (combined data-driven and mechanistic) models. This review will therefore support researchers intending to establish a chromatography modeling workflow in their laboratory.

Architectural and Technological Improvements to Integrated Bioprocess Models towards Real-Time Applications

Integrated or holistic process models may serve as the engine of a digital asset in a multistep-process digital twin. Concatenated individual-unit operation models are effective at propagating errors over an entire process, but are nonetheless limited in certain aspects of recent applications that prevent their deployment as a plausible digital asset, particularly regarding bioprocess development requirements. Sequential critical quality attribute tests along the process chain that form output–input (i.e., pool-to-load) relationships, are impacted by nonaligned design spaces at different scales and by simulation distribution challenges. Limited development experiments also inhibit the exploration of the overall design space, particularly regarding the propagation of extreme noncontrolled parameter values. In this contribution, bioprocess requirements are used as the framework to improve integrated process models by introducing a simplified data model for multiunit operation processes, increasing statistical robustness, adding a new simulation flow for scale-dependent variables, and describing a novel algorithm for extrapolation in a data-driven environment. Lastly, architectural and procedural requirements for a deployed digital twin are described, and a real-time workflow is proposed, thus providing a final framework for a digital asset in bioprocessing along the full product life cycle.

Prediction of the performance of pre-packed purification columns through machine learning

Pre-packed columns have been increasingly used in process development and biomanufacturing thanks to their ease of use and consistency. Traditionally, packing quality is predicted through rate models, which require extensive calibration efforts through independent experiments to determine relevant mass transfer and kinetic rate constants. Here we propose machine learning as a complementary predictive tool for column performance. A machine learning algorithm, extreme gradient boosting, was applied to a large data set of packing quality (plate height and asymmetry) for pre-packed columns as a function of quantitative parameters (column length, column diameter, and particle size) and qualitative attributes (backbone and functional mode). The machine learning model offered excellent predictive capabilities for the plate height and the asymmetry (90 and 93%, respectively), with packing quality strongly influenced by backbone (∼70% relative importance) and functional mode (∼15% relative importance), well above all other quantitative column parameters. The results highlight the ability of machine learning to provide reliable predictions of column performance from simple, generic parameters, including strategic qualitative parameters such as backbone and functionality, usually excluded from quantitative considerations. Our results will guide further efforts in column optimization, for example, by focusing on improvements of backbone and functional mode to obtain optimized packings.

Holistic Process Models: A Bayesian Predictive Ensemble Method for Single and Coupled Unit Operation Models

The coupling of individual models in terms of end-to-end calculations for unit operations in manufacturing processes is a challenging task. We present a probability distribution-based approach for the combined outcomes of parametric and non-parametric models. With this so-called Bayesian predictive ensemble, the statistical moments such as mean value and standard deviation can be accurately computed without any further approximation. It is shown that the ensemble of different model predictions leads to an uninformed prior distribution, which can be transformed into a predictive posterior distribution using Bayesian inference and numerical Markov Chain Monte Carlo calculations. We demonstrate the advantages of our method using several numerical examples. Our approach is not restricted to certain unit operations, and can also be used for the more robust interpretation and assessment of model predictions in general.

Model Transferability and Reduced Experimental Burden in Cell Culture Process Development Facilitated by Hybrid Modeling and Intensified Design of Experiments

Reliable process development is accompanied by intense experimental effort. The utilization of an intensified design of experiments (iDoE) (intra-experimental critical process parameter (CPP) shifts combined) with hybrid modeling potentially reduces process development burden. The iDoE can provide more process response information in less overall process time, whereas hybrid modeling serves as a commodity to describe this behavior the best way. Therefore, a combination of both approaches appears beneficial for faster design screening and is especially of interest at larger scales where the costs per experiment rise significantly. Ideally, profound process knowledge is gathered at a small scale and only complemented with few validation experiments on a larger scale, saving valuable resources. In this work, the transferability of hybrid modeling for Chinese hamster ovary cell bioprocess development along process scales was investigated. A two-dimensional DoE was fully characterized in shake flask duplicates (300 ml), containing three different levels for the cultivation temperature and the glucose concentration in the feed. Based on these data, a hybrid model was developed, and its performance was assessed by estimating the viable cell concentration and product titer in 15 L bioprocesses with the same DoE settings. To challenge the modeling approach, 15 L bioprocesses also comprised iDoE runs with intra-experimental CPP shifts, impacting specific cell rates such as growth, consumption, and formation. Subsequently, the applicability of the iDoE cultivations to estimate static cultivations was also investigated. The shaker-scale hybrid model proved suitable for application to a 15 L scale (1:50), estimating the viable cell concentration and the product titer with an NRMSE of 10.92% and 17.79%, respectively. Additionally, the iDoE hybrid model performed comparably, displaying NRMSE values of 13.75% and 21.13%. The low errors when transferring the models from shaker to reactor and between the DoE and the iDoE approach highlight the suitability of hybrid modeling for mammalian cell culture bioprocess development and the potential of iDoE to accelerate process characterization and to improve process understanding.

A novel framework of surrogate-based feasibility analysis for establishing design space of twin-column continuous chromatography

Multi-column periodic counter-current chromatography (PCC) has attracted wide attention for the primary capture for the purpose of achieving continuous biomanufacturing. Consequently, determining the design space of the continuous capture process is very important to facilitate process understanding and improving product quality. In this work, we proposed a novel approach to identify the design space of continuous chromatography to balance the computational complexity and model predictions. Specifically, surrogate-based feasibility analysis with adaptive sampling is applied to establish the design space of twin-column CaptureSMB process. The surrogate model is constructed based on the developed mechanistic model for the identification of the design space. The effects of process variables (including interconnected loading time, interconnected flowrate, and batch flowrate) on the design space are comprehensively examined based on an active set strategy. Besides, essential factors like recovery-regeneration time and constraints of column performance parameters (yield, productivity, and capacity utilization) are thoroughly investigated. The impact of design variables such as column length is also studied.

A Hybrid Modeling Framework for Membrane Separation Processes: Application to Lithium-Ion Recovery from Batteries

This study proposed a hybrid modeling framework for membrane separation processes where lithium from batteries is recovered. This is a pertinent problem nowadays as lithium batteries are popularized in hybrid and electric vehicles. The hybrid model is based on an artificial intelligence (AI) structure to model the mass transfer resistance of several experimental separations found in the literature. It is also based on a phenomenological model to represent the transient system regime. An optimization framework was designed to perform the AI model training and simultaneously solve the Ordinary Differential Equation (ODE) system representing the phenomenological model. The results demonstrate that the hybrid model can better represent the experimental validation sets than the phenomenological model alone. This strategy opens doors for further investigations of this system.

Design of Biopharmaceutical Formulations Accelerated by Machine Learning

In addition to activity, successful biological drugs must exhibit a series of suitable developability properties, which depend on both protein sequence and buffer composition. In the context of this high-dimensional optimization problem, advanced algorithms from the domain of machine learning are highly beneficial in complementing analytical screening and rational design. Here, we propose a Bayesian optimization algorithm to accelerate the design of biopharmaceutical formulations. We demonstrate the power of this approach by identifying the formulation that optimizes the thermal stability of three tandem single-chain Fv variants within 25 experiments, a number which is less than one-third of the experiments that would be required by a classical DoE method and several orders of magnitude smaller compared to detailed experimental analysis of full combinatorial space. We further show the advantage of this method over conventional approaches to efficiently transfer historical information as prior knowledge for the development of new biologics or when new buffer agents are available. Moreover, we highlight the benefit of our technique in engineering multiple biophysical properties by simultaneously optimizing both thermal and interface stabilities. This optimization minimizes the amount of surfactant in the formulation, which is important to decrease the risks associated with corresponding degradation processes. Overall, this method can provide high speed of converging to optimal conditions, the ability to transfer prior knowledge, and the identification of new nonlinear combinations of excipients. We envision that these features can lead to a considerable acceleration in formulation design and to parallelization of operations during drug development.