New trends in reversed-phase liquid chromatographic separations of therapeutic peptides and proteins: theory and applications

Preparation, characterization, and simulation of continuous stationary phase gradients on butyl functionalized liquid chromatography columns for protein and peptide separations

This work seeks to explore the capabilities of stationary phase gradients (SPGs) for the large-molecule chromatographic separations of proteins and peptides through a combination of experimental studies and simulations. Continuous SPGs are fabricated on commercial Phenomenex Jupiter C4 columns using the time-based infusion of trifluoroacetic acid through the column. The resultant gradients are characterized using small-molecule chromatography and physical gradient profiling via thermogravimetric analysis. The gradient columns are then tested using two different protein analyte mixtures and a peptide standard analyte mixture to examine the efficacy of the separations. Collected experimental data from these tests are used to establish fitted parameters for the Linear Solvent Strength (LSS) model to computationally predict the retention behavior of the analytes on the gradient columns. Successful chromatographic separation of all three analyte mixtures was achieved. The re-parameterized LSS model successfully simulates the analyte retention on the gradient columns with only minor deviations from observed experimental retention data. Collectively, this work demonstrates the ability to create a C4 continuous stationary phase gradient starting with a uniform commercial column that can be effectively used to separate mixtures of biomolecules, and the ability to accurately simulate and predict retention times. The computational model described herein could be used to effectively predict retention behavior in silico, significantly reducing the time needed for experimental design.

Peptide Property Prediction for Mass Spectrometry Using AI: An Introduction to State of the Art Models

This review explores state of the art machine learning and deep learning models for peptide property prediction in mass spectrometry-based proteomics, including, but not limited to, models for predicting digestibility, retention time, charge state distribution, collisional cross section, fragmentation ion intensities, and detectability. The combination of these models enables not only the in silico generation of spectral libraries but also finds many additional use cases in the design of targeted assays or data-driven rescoring. This review serves as both an introduction for newcomers and an update for experienced researchers aiming to develop accessible and reproducible models for peptide property predictions. Key limitations of the current models, including difficulties in handling diverse post-translational modifications and instrument variability, highlight the need for large-scale, harmonized datasets, and standardized evaluation metrics for benchmarking.

Design and development of a modular centrifugal platform with adjustable mixing and automated position-switching for stepwise gradient elution in reversed-phase liquid chromatography

This study introduces a modular centrifugal platform developed for stepwise gradient elution in reversed-phase liquid chromatography, featuring adjustable mixing and automated position-switching mechanisms. Traditional methods of gradient elution rely on precision syringes and mixers to control eluent composition, but incorporating external pumping systems into centrifugal platforms presents substantial technical and economic challenges. To overcome these limitations, an adjustable eluent mixer was designed to generate concentration gradients by utilizing Coriolis-induced metering and shake-mode mixing processes. The eluent composition was controlled by varying the platform's rotational speed, with the effects of geometric and operational parameters on liquid distribution thoroughly analyzed. An operating curve was established to correlate methanol-water eluent compositions with rotational speed. Furthermore, a switchable fraction collector capable of automated position switching was developed to collect eluates from each elution step. By synchronizing rotational speed with ratchet-driven movements, the outer ring containing multiple fraction collectors rotates relative to the inner disk, enabling efficient replacement of filled collectors. Experimental results demonstrated the successful separation and collection of water-soluble dyes, highlighting the platform's potential as a cost-effective and precise solution for chromatographic applications.

Accelerated vaccine process development by orthogonal protein characterization

The COVID-19 pandemic altered the vaccine development paradigm with accelerated timelines from concept through clinical safety and efficacy. Characterization and release assays for vaccine programs were developed under similar time constraints to support bioprocess development, scaleup and formulation. During the development of these vaccines, SARS-CoV-2 variants of concern (VOCs) emerged requiring integration of additional antigens into the target product profile. Biochemical testing to support the addition of new antigen variants (identity, quantity, antigenicity/potency) needed substantial re-development. Here we present a reversed-phase high-performance liquid-chromatography method for antigen purity with orthogonal identification characterization comprising of Simple Wes and liquid-chromatography tandem mass spectrometry (LC/MS/MS) to support accelerated process development for recombinant protein vaccines. This suite of assays was deployed to support rapid, scientific decision-making enabling the transition from completion of a placebo-controlled dose-ranging Phase 2 study to the start of the global Phase 3 safety and efficacy trial in less than 2 weeks.

Umbrella Sampling MD Simulations for Retention Prediction in Peptide Reversed-phase Liquid Chromatography

Reversed-phase liquid chromatography (RPLC) is an essential tool for separating complex mixtures such as proteolytic digests in bottom-up proteomics. There is growing interest in methods that can predict the RPLC retention behavior of peptides and other analytes. Already, existing algorithms provide excellent performance based on empirical rules or large sets of RPLC training data. Here we explored a new type of retention prediction strategy that relies on first-principles modeling of peptide interactions with a C18 stationary phase. We recently demonstrated that molecular dynamics (MD) simulations can provide atomistic insights into the behavior of peptides under RPLC conditions (Anal. Chem. 2023, 95, 3892). However, the current work found that it is problematic to use conventional MD data for retention prediction, evident from a poor correlation between experimental retention times and MD-generated "fraction bound" values. We thus turned to umbrella sampling MD, a complementary technique that has previously been applied to probe noncovalent contacts in other types of systems. By restraining the peptide dynamic motions at various positions inside a C18-lined pore, we determined the free energy of the system as a function of peptide-stationary phase distance. ΔGbinding values determined in this way under various mobile phase conditions were linearly correlated with experimental retention times of tryptic test peptides. This work opens retention prediction avenues for novel types of stationary and mobile phases, and for peptides (or other analytes) having arbitrary chemical properties, without the need for RPLC reference data. Umbrella sampling can be used as a stand-alone tool, or it may serve to enhance existing retention prediction algorithms.

Decoding the Challenges: navigating Intact Peptide Mass Spectrometry-Based Analysis for Biological Applications

Quantitative analysis of peptides in biological fluids offers a high diagnostic and prognostic tool to reflect the pathophysiological condition of the patient. Recently, methods based on liquid chromatography coupled with mass spectrometry (LC-MS) for the quantitative determination of intact peptides have been replacing traditionally used ligand-binding assays, which suffer from cross-reactivity issues. The use of "top-down" analysis of peptides is rapidly increasing since it does not undergo incomplete or non-reproducible digestion like "bottom-up" approaches. However, the low abundance of peptides and their peculiar characteristics, as well as the complexity of biological fluids, make their quantification challenging. Herein, the analytical pitfalls that may be encountered during the development of an LC-MS method for the analysis of intact peptides in biological fluids are discussed. Challenges in the pre-analytical phase, stability after sampling and sample processing, significantly impact the accuracy of peptide quantification. Emerging techniques, such as microextractions, are becoming crucial for improved sample cleanup and enrichment of target analytes. A comparison between the roles of high-resolution and low-resolution mass spectrometry in the quantification of intact peptides, as well as the introduction of supercharging reagents to enhance ionization, will be discussed.

Greening Separation and Purification of Proteins and Peptides

The increasing awareness of environmental issues and the transition to green analytical chemistry (GAC) have gained popularity among academia and industry in recent years. One of the principles of GAC is the reduction and replacement of toxic solvents with more sustainable and environmentally friendly ones. This review gives an overview of the advances in applying green solvents as an alternative to the traditional organic solvents for peptide and protein purification and analysis by liquid chromatography (LC) and capillary electrophoresis (CE) methods. The feasibility of using greener LC and CE methods is demonstrated through several application examples; however, there is still plenty of room for new developments to fully realize their potential and to address existing challenges. Thanks to the tunable properties of designer solvents, such as ionic liquids and deep eutectic solvents, and almost infinite possible mixtures of components for their production, it is possible that some new designer solvents could potentially surpass the traditional harmful solvents in the future. Therefore, future research should focus mainly on developing new solvent combinations and enhancing analytical instruments to be able to effectively work with green solvents.

A stability-indicating method development and validation for the determination of related substances in novel synthetic decapeptide by HPLC

In the present scenario, peptide is an emerging field of research having vast therapeutic applications. Diverse impurities may rise from various stages of the synthesis process and storage of the peptides. Because these contaminants may have an impact on the therapeutic safety and effectiveness of peptides in their approaching applications, they must be identified and carefully monitored. Considering the pharmaceutical importance of the extent of peptides, we were motivated to synthesize a decapeptide and establish a novel gradient reversed-phase high-performance liquid chromatography (RP-HPLC) method for its analysis along with efficient separation of its six related impurities. Different buffers, organic modifiers, and columns were used in the tests for good separation of these impurities. To establish a stability-indicating method, a stress study was also conducted. The International Conference on Harmonization (ICH) guidelines have been followed for validation of the developed analytical method. The validated method revealed sufficient accuracy, specificity, linearity, robustness, precision, and high sensitivity for its intended use. The proposed method could be appropriate for routine analysis and stability assessment of the decapeptide, which might be useful for further scientific investigation.

Large-scale purification of a deprotected macrocyclic peptide by supercritical fluid chromatography (SFC) integrated with liquid chromatography in discovery chemistry

A macrocyclic peptide A was successfully purified in large quantities (∼30 g) in >95 % purity by an integrated two-step orthogonal purification process combining supercritical fluid chromatography (SFC) with medium-pressure reverse-phase liquid chromatography (MP-RPLC). MP-RPLC was used to fractionate the crude peptide A, remove unwanted trifluoroacetic acid (TFA) originating from the peptide A cleavage off the resin, and convert the peptide A into ammonium acetate salt form, prior to the final purification by SFC. A co-solvent of methanol/acetonitrile containing ammonium acetate and water in CO2 was developed on a Waters BEH 2-Ethylpyridine column. The developed SFC method was readily scaled up onto a 5 cm diameter column to process multi-gram quantities of the MP-RPLC fraction to reach > 95 % purity with a throughput/productivity of 0.96 g/h. The incorporation of SFC with MP-RPLC has been demonstrated to have a broader application in other large-scale polypeptide purifications.

Development of a high-throughput liquid chromatography-tandem mass spectrometry platform for the determination of intact natriuretic peptides in human plasma

We present an innovative, reliable, and antibody-free analytical method to determine multiple intact natriuretic peptides in human plasma. These biomolecules are routinely used to confirm the diagnosis and monitor the evolution of heart failure, so that their determination is essential to improve diagnosis and monitor the efficacy of treatment. However, common immunoassay kits suffer from main limitations due to high cross-reactivity with structurally similar species. In our method, we pre-treated the sample by combining salting-out with ammonium sulfate with microextraction by packed sorbent technique. Analyses were then carried out by ultra-high performance liquid chromatography-electrospray ionization-tandem mass spectrometry. The use of 3-nitrobenzyl alcohol as a supercharger reagent enhanced the ESI ionization and improved the signal-to-noise ratio. The analytical protocol showed good linearity over one order of magnitude, recovery in the range of 94-105 %, and good intra- and inter-day reproducibility (RSD<20 %), and the presence of a matrix effect. Limits of detection were in the range of pg/mL for all peptides (0.2-20 pg/mL). Stability study in plasma samples demonstrated that proper protease inhibitors need to be included in blood collection tubes to avoid peptide degradation. Preliminary analyses on plasma samples from heart failure patients allow the quantification of ANP 1-28 as the most abundant species and the detection of ANP 5-28, BNP 1-32, and BNP 5-32. The method could be used to investigate how cross-reactivity issues among structurally similar species impact determinations by ELISA kits.

Recent Advances in the Field of Amino Acid-Conjugated Aminoferrocenes-A Personal Perspective

The development of turn-based inhibitors of protein-protein interactions has attracted considerable attention in medicinal chemistry. Our group has synthesized a series of peptides derived from an amino-functionalized ferrocene to investigate their potential to mimic protein turn structures. Detailed DFT and spectroscopic studies (IR, NMR, CD) have shown that, for peptides, the backbone chirality and bulkiness of the amino acid side chains determine the hydrogen-bond pattern, allowing tuning of the size of the preferred hydrogen-bonded ring in turn-folded structures. However, their biological potential is more dependent on their lipophilicity. In addition, our pioneering work on the chiroptical properties of aminoferrocene-containing peptides enables the correlation of their geometry with the sign of the CD signal in the absorption region of the ferrocene chromophore. These studies have opened up the possibility of using aminoferrocene and its derivatives as chirooptical probes for the determination of various chirality elements, such as the central chirality of amino acids and the helicity of peptide sequences.

Automated high-throughput buffer exchange platform enhances rapid flow analysis of antibody drug conjugates by high resolution mass spectrometry

Antibody drug conjugates (ADCs) are an increasingly important therapeutic class of molecules for the treatment of cancer. Average drug-to-antibody ratio (DAR) and drug-load distribution are critical quality attributes of ADCs with the potential to impact efficacy and toxicity of the molecule and need to be analytically characterized and understood. Several platform methods including hydrophobic interaction chromatography (HIC) and native size-exclusion chromatography-mass spectrometry (nSEC-MS) have been developed for that purpose; however, each presents some limitations. In this work, we assessed a new sample preparation and buffer exchange platform coupled with high-resolution mass spectrometry for characterizing the drug-load and distribution of several cysteine-linked ADCs conjugated with a variety of chemotypes. Several criteria were evaluated during the optimization of the buffer exchange-mass spectrometry system performance and the data generated with the system were compared with results from nSEC-MS and HIC. The results indicated that the platform enables automated and high throughput quantitative DAR characterization for antibody-drug conjugates with high reproducibility and offers several key advantages over existing approaches that are used for chemotype-agnostic ADC characterization.

Imidazole-octyl mixed-mode stationary phase based on macroporous silica for the purification of ovomucoid and ovotransferrin

A process-simplified hard template approach was established to synthesize the monodisperse macroporous silica microspheres with homogeneous structures by twice alkali-thermal treatment and calcination routes. Porous vinyl-functionalized polysesquioxane microspheres (V-PMSQ) were synthesized through a hydrolyzation-polycondensation method and used as templates. The template particles with large aperture and high pore volume were obtained by adjusting the pH value and reaction time of the twice alkali-thermal reaction. After calcination, monodisperse silica microspheres with an average pore size of 30 nm, homogeneous pore structures, and narrow particle size distribution were fabricated, which can be directly used as chromatographic matrices without classification. After that, a new reversed-phase/strong anion-exchange (RP/SAX) mixed-mode stationary phase Sil-S-VOIM was prepared by bonding the 1-vinyl-3-octyl-imidazole ligands to the above silica microspheres through a "thiol-ene" click reaction. The performance of the Sil-S-VOIM column was evaluated by one acidic protein (transferrin) and two basic proteins (lysozyme, α-chymotrypsin) and compared to a single imidazole-modified Sil-S-VIM column and an octyl-modified Sil-C8 column, respectively. Due to the synergistic effect of electrostatic repulsion and hydrophobic interactions, baseline separations of the above proteins were observed only on the Sil-S-VOIM column, with resolutions of 2.55 and 2.01 between lysozyme and transferrin, and between transferrin and α-chymotrypsin, respectively, indicating good selectivity and separation ability compared with single-mode stationary phases. It was applied to the isolation of egg white samples with peaks identified by SDS-PAGE and MALDI-TOF-MS. The results showed that the selective retention and isolation of ovomucoid and ovotransferrin were successfully achieved, with yields of 78.8% and 67.2%, respectively. The protocol described in this work is simpler, faster, and has higher protein recovery. Overall, this new mixed-mode stationary phase provided a promising potential for the separation and determination of intact proteins.

Advances in AI-Driven Retention Prediction for Different Chromatographic Techniques: Unraveling the Complexity

Retention prediction through Artificial intelligence (AI)-based techniques has gained exponential growth due to their abilities to process complex sets of data and ease the crucial task of identification and separation of compounds in most employed chromatographic techniques. Numerous approaches were reported for retention prediction in different chromatographic techniques, and consistent results demonstrated that the accuracy and effectiveness of deep learning models outclassed the linear machine learning models, mainly in liquid and gas chromatography, as ML algorithms use fewer complex data to train and predict information. Support Vector machine-based neural networks were found to be most utilized for the prediction of retention factors of different compounds in thin-layer chromatography. Cheminformatics, chemometrics, and hybrid approaches were also employed for the modeling and were more reliable in retention prediction over conventional models. Quantitative Structure Retention Relationship (QSRR) was also a potential method for predicting retention in different chromatographic techniques and determining the separation method for analytes. These techniques demonstrated the aids of incorporating QSRR with AI-driven techniques acquiring more precise retention predictions. This review aims at recent exploration of different AI-driven approaches employed for retention prediction in different chromatographic techniques, and due to the lack of summarized literature, it also aims at providing a comprehensive literature that will be highly useful for the society of scientists exploring the field of AI in analytical chemistry.

Current trends in chromatographic prediction using artificial intelligence and machine learning

Artificial intelligence (AI) and machine learning (ML) gained tremendous growth and are rapidly becoming popular in various fields of prediction due to their potential abilities, accuracy, and speed. Machine learning algorithms employ historical data to analyze or predict information using patterns or trends. AI and ML were most employed in chromatographic predictions and particularly attractive options for liquid chromatography method development, as they can help achieve desired results faster, more accurately, and more efficiently. This review aims at exploring various AI and ML models employed in the determination of chromatographic characteristics. This review also aims to provide deep insight into reported artificial neural network (ANN) associated techniques which maintained better accuracy and significant possibilities for chromatographic characteristics prediction in liquid chromatography over classical linear models and also emphasizes the integration of a fuzzy system with an ANN, as this integrated study provides more efficient and accurate methods in chromatographic prediction than other linear models. This study also focuses on the retention prediction of a target molecule employing QSRR methodology combined with an ANN, highlighting a more effective technique than the QSRR alone. This approach showed the benefits of combining AI or ML algorithms with the QSRR to obtain more accurate retention predictions, emphasizing the potential of artificial intelligence and machine learning for overcoming adversities in analytical chemistry.

Atomistic Details of Peptide Reversed-Phase Liquid Chromatography from Molecular Dynamics Simulations

Peptide separations by reversed-phase liquid chromatography (RPLC) are an integral part of bottom-up proteomics. These separations typically employ C18 columns with water/acetonitrile gradient elution in the presence of formic acid. Despite the widespread use of such workflows, the exact nature of peptide interactions with the stationary and mobile phases is poorly understood. Here, we employ microsecond molecular dynamics (MD) simulations to uncover details of peptide RPLC. We examined two tryptic peptides, a hydrophobic and a hydrophilic species, in a slit pore lined with C18 chains that were grafted onto SiO₂ support. Our simulations explored peptide trapping, followed by desorption and elution. Trapping in an aqueous mobile phase was initiated by C18 contacts with Lys butyl moieties. This was followed by extensive anchoring of nonpolar side chains (Leu/Ile/Val) in the C18 layer. Exposure to water/acetonitrile triggered peptide desorption in a stepwise fashion; charged sites close to the termini were the first to lift off, followed by the other residues. During water/acetonitrile elution, both peptides preferentially resided close to the pore center. The hydrophilic peptide exhibited no contacts with the stationary phase under these conditions. In contrast, the hydrophobic species underwent multiple transient Leu/Ile/Val binding interactions with C18 chains. These nonpolar interactions represent the foundation of differential peptide retention, in agreement with the experimental elution behavior of the two peptides. Extensive peptide/formate ion pairing was observed in water/acetonitrile, particularly at N-terminal sites. Overall, this work uncovers an unprecedented level of RPLC molecular details, paving the way for MD simulations as a future tool for improving retention prediction algorithms and for the design of novel column materials.

Quantification of Dolichyl Phosphates Using Phosphate Methylation and Reverse-Phase Liquid Chromatography-High Resolution Mass Spectrometry

Dolichyl monophosphates (DolPs) are essential lipids in glycosylation pathways that are highly conserved across almost all domains of life. The availability of DolP is critical for all glycosylation processes, as these lipids serve as membrane-anchored building blocks used by various types of glycosyltransferases to generate complex post-translational modifications of proteins and lipids. The analysis of DolP species by reverse-phase liquid chromatography-mass spectrometry (RPLC-MS) remains a challenge due to their very low abundance and wide range of lipophilicities. Until now, a method for the simultaneous qualitative and quantitative assessment of DolP species from biological membranes has been lacking. Here, we describe a novel approach based on simple sample preparation, rapid and efficient trimethylsilyl diazomethane-dependent phosphate methylation, and RPLC-MS analysis for quantification of DolP species with different isoprene chain lengths. We used this workflow to selectively quantify DolP species from lipid extracts derived of Saccharomyces cerevisiae, HeLa, and human skin fibroblasts from steroid 5-α-reductase 3- congenital disorders of glycosylation (SRD5A3-CDG) patients and healthy controls. Integration of this workflow with global lipidomics analyses will be a powerful tool to expand our understanding of the role of DolPs in pathophysiological alterations of metabolic pathways downstream of HMG-CoA reductase, associated with CDGs, hypercholesterolemia, neurodegeneration, and cancer.

LC-MS/MS method for the quantitation of serum tocilizumab in rheumatoid arthritis patients using rapid tryptic digestion without IgG purification

The quantitation of serum tocilizumab using liquid chromatography tandem-mass spectrometry (LC-MS/MS) method has not been widely applied in clinical settings because of its time-consuming and costly sample pretreatments. The present study aimed to develop a validated LC-MS/MS method for detecting serum tocilizumab by utilizing immobilized trypsin without an immunoglobulin G purification step and evaluate its applicability in the treatment of rheumatoid arthritis (RA) patients administered intravenously or subcutaneously with tocilizumab. The tocilizumab-derived signature peptide was deciphered using a nano-LC system coupled to a hybrid quadrupole-orbitrap mass spectrometer. The serum tocilizumab was rapidly digested by immobilized trypsin for 30 min. The chromatographic peak of the signature peptide and that of the internal standard were separated from the serum digests for a total run time of 15 min. The calibration curve of serum tocilizumab concentration was linear with a range of 2-200 μg/mL. The intra- and inter-day accuracy and relative standard deviation (RSD) were 90.7%-109.4% and <10%, respectively. The serum tocilizumab concentrations in the RA patients receiving intravenous and subcutaneous injections were 5.8-28.9 and 2.4-63.5 μg/mL, respectively. The serum tocilizumab concentrations using the current method positively correlated with those using the enzyme-linked immunosorbent assay, although a systematic error was observed between these methods. In conclusion, a validated LC-MS/MS method with minimal sample pretreatments for monitoring serum tocilizumab concentrations in RA patients was developed.

Proteomics Characterization of Food-Derived Bioactive Peptides with Anti-Allergic and Anti-Inflammatory Properties

Bioactive peptides are found in foods and dietary supplements and are responsible for health benefits with applications in human and animal medicine. The health benefits include antihypertensive, antimicrobial, antithrombotic, immunomodulatory, opioid, antioxidant, anti-allergic and anti-inflammatory functions. Bioactive peptides can be obtained by microbial action, mainly by the gastrointestinal microbiota from proteins present in food, originating from either vegetable or animal matter or by the action of different gastrointestinal proteases. Proteomics can play an important role in the identification of bioactive peptides. High-resolution mass spectrometry is the principal technique used to detect and identify different types of analytes present in complex mixtures, even when available at low concentrations. Moreover, proteomics may provide the characterization of epitopes to develop new food allergy vaccines and the use of immunomodulating peptides to induce oral tolerance toward offending food allergens or even to prevent allergic sensitization. In addition, food-derived bioactive peptides have been investigated for their anti-inflammatory properties to provide safer alternatives to nonsteroidal anti-inflammatory drugs (NSAIDs). All these bioactive peptides can be a potential source of novel drugs and ingredients in food and pharmaceuticals. The following review is focused on food-derived bioactive peptides with antiallergic and anti-inflammatory properties and summarizes the new insights into the use of proteomics for their identification and quantification.

A story of peptides, lipophilicity and chromatography - back and forth in time

Peptides, as part of the beyond the rule of 5 (bRo5) chemical space, represent a unique class of pharmaceutical compounds. Because of their exceptional position in the chemical space between traditional small molecules (molecular weight (MW) < 500 Da) and large therapeutic proteins (MW > 5000 Da), peptides became promising candidates for targeting challenging binding sites, including even targets traditionally considered as undruggable - e.g. intracellular protein-protein interactions. However, basic knowledge about physicochemical properties that are important for a drug to be membrane permeable is missing but would enhance the drug discovery process of bRo5 molecules. Consequently, there is a demand for quick and simple lipophilicity determination methods for peptides. In comparison to the traditional lipophilicity determination methods via shake flask and in silico prediction, chromatography-based methods could have multiple benefits such as the requirement of low analyte amount, insensitivity to impurities and high throughput. Herein we elucidate the role of peptide lipophilicity and different lipophilicity values. Further, we summarize peptide analysis via common chromatographic techniques, in specific reversed phase liquid chromatography, hydrophilic interaction liquid chromatography and supercritical fluid chromatography and their role in drug discovery and development process.

Preparation of mixed-mode stationary phase for separation of peptides and proteins in high performance liquid chromatography

Porous silica particles were prepared by sol–gel method with some modification to get wide-pore particles. These particles were derivatized with N-phenylmaleimide-methylvinylisocyanate (PMI) and styrene by reversible addition fragmentation chain transfer (RAFT) polymerization to prepare N-phenylmaleimide embedded polystyrene (PMP) stationary phases. Narrow bore stainless steel column (100 × 1.8 mm i.d) was packed by slurry packing method. The chromatographic performance of PMP column was evaluated for the separation of synthetic peptides mixture composed of five peptides (Gly-Tyr, Gly-Leu-Tyr, Gly-Gly-Tyr-Arg, Tyr-Ile-Gly-Ser-Arg, Leucine enkephalin) and tryptic digest of human serum albumin (HAS) respectively. Number of theoretical plates as high as 280,000 plates/m were obtained for peptides mixture at optimum elution condition. Separation performance of the developed column was compared with commercial Ascentis Express RP-Amide column and it was observed that separation performance of PMP column was better than commercial column in terms of separation efficiency and resolution.

Comparison of the separation of proteins of wide-ranging molecular weight via trilobal polypropylene capillary-channeled polymer fiber, commercial superficiously porous, and commercial size exclusion columns

Reversed phase and size-exclusion chromatography methods are commonly used for protein separations, though based on distinctly different principles. Reversed phase methods yield hydrophobicity-based (loosely-termed) separation of proteins on porous supports, but tend to be limited to proteins with modest molecular weights based on mass transfer limitations. Alternatively, size-exclusion provides complementary benefits in the separation of higher-mass proteins based on entropic, not enthalpic, processes, but tend to yield limited peak capacities. In this study, microbore columns packed with a novel trilobal polypropylene capillary-channeled polymer fiber were used in a reversed phase modality for the separation of polypeptides and proteins of molecular weights ranging from 1.4 to 660 kDa. Chromatographic parameters including gradient times, flow rates and trifluoroacetic acid concentrations in the mobile phase were optimized to maximize resolution and throughput. Following optimization, the performance of the trilobal fiber column was compared to two commercial-sourced columns, a superficially porous C4-derivatized silica and size exclusion, both of which are sold specifically for protein separations and operated according to the manufacturer-specified conditions. In comparison to the commercial columns, the fiber-based column yielded better separation performance across the entirety of the suite, at much lower cost and shorter separation times. This article is protected by copyright. All rights reserved.

Analysis of short-chain bioactive peptides by unified chromatography-electrospray ionization mass spectrometry. Part II. Comparison to reversed-phase ultra-high performance liquid chromatography

In the first part of this study, a unified chromatography (UC) analysis method, which is similar to supercritical fluid chromatography (SFC) but with wide mobile phase gradients of pressurized CO₂ and solvent, was developed to analyse short-chain peptides, with UV and mass spectrometry (MS) detection. In this second part, the method is compared to a reference reversed-phase ultra-high-performance liquid chromatography (RP-UHPLC) method, based on the analysis of 43 peptides, including 10 linear peptides and 33 cyclic ones. First, the orthogonality between the two methods was examined, based on the retention patterns. As the UC method was developed on a polar stationary phase (Ascentis Express OH5), the elution orders and selectivities were expected to be significantly different from RPLC on a non-polar stationary phase (ACQUITY CSH C18). Secondly, the success rate of the methods was examined, based on successful retention / elution of the peptides and the absence of observed co-elutions between the main peak and impurities. A successful analysis was obtained for 81% of the peptides in UC and 67% in RPLC. Thirdly, the performance of the methods for the intended application of impurity profiling of peptide drug candidates was assessed, based on the comparison of peak purities, the number of impurities detected and the thorough examination of impurity profiles. Excellent complementarity of the two methods for the specific task of impurity profiling, and for the separation of isomeric species was observed, with only one isomeric pair in this set remaining unresolved. The method sensitivity was however better with RPLC than UC. Finally, the operational costs in terms of solvent cost per analysis were the same between the two methods.

Downstream Processing of Therapeutic Peptides by Means of Preparative Liquid Chromatography

The market of biomolecules with therapeutic scopes, including peptides, is continuously expanding. The interest towards this class of pharmaceuticals is stimulated by the broad range of bioactivities that peptides can trigger in the human body. The main production methods to obtain peptides are enzymatic hydrolysis, microbial fermentation, recombinant approach and, especially, chemical synthesis. None of these methods, however, produce exclusively the target product. Other species represent impurities that, for safety and pharmaceutical quality reasons, must be removed. The remarkable production volumes of peptide mixtures have generated a strong interest towards the purification procedures, particularly due to their relevant impact on the manufacturing costs. The purification method of choice is mainly preparative liquid chromatography, because of its flexibility, which allows one to choose case-by-case the experimental conditions that most suitably fit that particular purification problem. Different modes of chromatography that can cover almost every separation case are reviewed in this article. Additionally, an outlook to a very recent continuous chromatographic process (namely Multicolumn Countercurrent Solvent Gradient Purification, MCSGP) and future perspectives regarding purification strategies will be considered at the end of this review.

At-Line Reversed Phase Liquid Chromatography for In-Process Monitoring of Inclusion Body Solubilization

Refolding is known as the bottleneck in inclusion body (IB) downstream processing in the pharmaceutical industry: high dilutions leading to large operating volumes, slow refolding kinetics and low refolding yields are only a few of the problems that impede industrial application. Solubilization prior to refolding is often carried out empirically and the effects of the solubilizate on the subsequent refolding step are rarely investigated. The results obtained in this study, however, indicate that the quality of the IB solubilizate has a severe effect on subsequent refolding. As the solubilizate contains chaotropic reagents in high molarities, it is commonly analyzed with sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). SDS-PAGE, however, suffers from a long analysis time, making at-line analytical implementation difficult. In this study, we established an at-line reversed phase liquid chromatography method to investigate the time-dependent quality of the solubilizate. To verify the necessity of at-line solubilization monitoring, we varied the essential solubilization conditions for horseradish peroxidase IBs. The solubilization time was found to have a major influence on subsequent refolding, underlining the high need for an at-line analysis of solubilization. Furthermore, we used the developed reversed phase liquid chromatography method for an in-process control (IPC). In conclusion, the presented reversed phase liquid chromatography method allows a proper control of IB solubilization applicable for tailored refolding.

Establishment of validated stability indicating purity method based on the stress degradation behavior of gonadotropin-releasing hormone antagonist (ganirelix) in an injectable formulation using HPLC and LC-MS-QTOF

Stress study of a drug substance or pharmaceutical drug product provides a vision into degradation pathways and degradation products of the active pharmaceutical ingredient and helps in interpretation of the chemical structure of the degradation impurities. In the current study, Ganirelix active ingredient presented in the Orgalutran® was stressed with acidic and alkali hydrolysis, photolysis, thermal and oxidation conditions as per the guidelines of International Conference on Harmonization (ICH) Q1A (R2). Ganirelix was found to be labile under thermal and alkali hydrolytic stress conditions, while it was stable to acid hydrolytic, oxidative and photolytic stress. All degradation products were separated with a resolution > 1.5 on a C18 column (2.6 µm, 25 cm×4.6 mm) using a hydrophilic ion pair such as sodium perchlorate, at a concentration <0.04 M. In total, four major degradant impurities were found during stress study. These impurities were fractionated and desalted by flash chromatography for identification of chemical structures. LC-MS-QTOF analysis revealed that two degradation products are diastereomers of Ganirelix, one degradation product is a deamination compound and other degradation product result from the insertion of a new amino acid residue in the Ganirelix peptide sequence. The developed method is sensitive enough to quantify the related substances of Ganirelix at the 0.04% level with that of Ganirelix test concentration.

Trends in the Analysis of Biopharmaceuticals by HPLC

Background:

Biopharmaceuticals are biological drugs consisting of a complex compound that can be produced by a living organism or derive from it. Biopharmaceuticals are very complicated compounds from structural point of view and for this reason, they cannot be fully characterized in terms of their structure with current analytical methods as it happens instead of low molecular weight chemicals drugs.

Introduction:

The regulatory guidelines require the characterization of the primary or higher sequence of these molecules and the characterization of any post-translational modifications. The use of biopharmaceuticals has really grown in the last few years: in 2016, the number of biopharmaceuticals approved by the Food and Drug Administration (FDA) and European Medicines Agency (EMA) for use in humans’ diseases was 1357. From 2013 to 2016, 73 of these compounds were approved for the treatment of cancer, inflammation, immune disorders, infections, anemia and cardiovascular diseases.

Aim/Conclusion:

The aim of the present review is to provide an overview of recent approaches for the characterization of biopharmaceutical products in HPLC that have been presented in the literature in the last years.

Microfluidics Chip for Directional Solvent Extraction Desalination of Seawater

Directional solvent extraction is one of the promising membrane-less seawater desalination method. This technique was not extensively investigated due the poor mixing and separation performances of its bench-scale system. It is believed that, overcoming these drawbacks is possible now with the rapid development of microfluidics technology that enabled high-precession micro mixing and separation. This work presents microfluidics chip for extracting and separating salt from seawater. The chip was designed with two sections for extraction and separation. In both sections, the liquids were separated using capillary channels perpendicular to the main stream. The main channels were designed to be 400 µm in width and 100 µm in height. Two streams inlets were introduced through a Y-junction containing octanoic acid as the organic phase and saltwater as the aqueous phase. The desalination performance was investigated at four different temperatures and five different solvent flow rates. Water product salinity was recorded to be as low as 0.056% (w/w) at 60 °C and 40 mL/h. A maximum water yield of 5.2% was achieved at 65 °C and 40 mL/h with a very low solvent residual (70 ppm). The chip mass transfer efficiency was recorded to be as high as 68% under similar conditions. The fabricated microfluidic desalination system showed a significant improvement in terms of water yield and separation efficiency over the conventional macroscale. The high performance of this microsystem resulted from its ability to achieve a high mixing efficiency and separate phases selectively and that will provide a good platform in the near future to develop small desalination kits for personal use.

Sub-picomolar quantification of PTH 1-34 in plasma by UHPLC-MS/MS after subcutaneous injection of teriparatide and identification of PTH 1-33, its degradation product

Teriparatide (PTH 1-34, Forsteo^®) is a bioactive N-terminal fragment of the native endogenous parathyroid hormone (PTH 1-84) recommended for the treatment of osteoporosis in patients with high risk of fracture. Since PTH 1-34 may undergo proteolysis we have validated an ultra-high pressure liquid chromatography tandem mass spectrometry (UHPLC-MS/MS) method for unambiguously measuring intact PTH 1-34 with the same sensitivity as ELISA, at subpicomolar level (LLOQ at 0.4 pM). The full chromatographic run was achieved in 16.5 min. The method validation showed satisfactory intra- and inter-assay precision (CV < 13%) and excellent trueness (<5%), and almost no matrix effect (recoveries 78-92%). We found that after subcutaneous injection in two volunteers, PTH 1-34 half-life was shorter with UHPLC-MS/MS and that ELISA was overestimating PTH 1-34 late concentrations in both volunteers. Qualitative mass spectrometry was performed and led to the discovery of PTH 1-33, a fragment of PTH 1-34 with unknown function. This study emphasized the importance of switching from immunoassays to mass spectrometry when measuring bioactive peptides prompt to proteolysis into fragments that may exhibit altered bioactivity and duration of action.

Artificial Neural Network Prediction of Retention of Amino Acids in Reversed-Phase HPLC under Application of Linear Organic Modifier Gradients and/or pH Gradients

A multi-layer artificial neural network (ANN) was used to model the retention behavior of 16 o-phthalaldehyde derivatives of amino acids in reversed-phase liquid chromatography under application of various gradient elution modes. The retention data, taken from literature, were collected in acetonitrile⁻water eluents under application of linear organic modifier gradients ( gradients), pH gradients, or double pH/ gradients. At first, retention data collected in  gradients and pH gradients were modeled separately, while these were successively combined in one dataset and fitted simultaneously. Specific ANN-based models were generated by combining the descriptors of the gradient profiles with 16 inputs representing the amino acids and providing the retention time of these solutes as the response. Categorical "bit-string" descriptors were adopted to identify the solutes, which allowed simultaneously modeling the retention times of all 16 target amino acids. The ANN-based models tested on external gradients provided mean errors for the predicted retention times of 1.1% ( gradients), 1.4% (pH gradients), 2.5% (combined  and pH gradients), and 2.5% (double pH/ gradients). The accuracy of ANN prediction was better than that previously obtained by fitting of the same data with retention models based on the solution of the fundamental equation of gradient elution.

Fundamental Properties of Packing Materials for Liquid Chromatography

The high performance of chemically-modified silica gel packing materials is based on the utilization of pure silica gels. Earlier silica gels used to be made from inorganic silica; however, nowadays, silica gels are made from organic silanes. The surface smoothness and lack of trace metals of new silica gels permits easy surface modifications (chemical reactions) and improves the reproducibility and stability. Sharpening peak symmetry is based on developing better surface modification methods (silylation). Typical examples can be found in the chromatography of amitriptyline for silanol testing and that of quinizarin for trace metal testing. These test compounds were selected and demonstrated sensitive results in the measurement of trace amounts of either silanol or trace metals. Here, we demonstrate the three-dimensional model chemical structures of bonded-phase silica gels with surface electron density for easy understanding of the molecular interaction sites with analytes. Furthermore, a quantitative explanation of hydrophilic and hydrophobic liquid chromatographies was provided. The synthesis methods of superficially porous silica gels and their modified products were introduced.

Enhanced-Fluidity Liquid Chromatography-Mass Spectrometry for Intact Protein Separation and Characterization

Recent advances in the analysis of proteins have increased the demand for more efficient techniques to separate intact proteins. Enhanced-fluidity liquid chromatography (EFLC) involves the addition of liquefied CO₂ to conventional liquid mobile phases. The addition of liquefied CO₂ increases diffusivity and decreases viscosity, which inherently leads to a more efficient separation. Herein, EFLC is applied to hydrophobic interaction chromatography (HIC) stationary phases for the first time to study the impact of liquefied CO₂ to the chromatographic behavior of proteins. The effects of liquefied CO₂ on chromatographic properties, charge state distributions (CSDs), and ionization efficiencies were evaluated. EFLC offered improved chromatographic performance compared to conventional liquid chromatography (LC) methods including a shorter analysis time, better peak shapes, and higher plate numbers. The addition of liquefied CO₂ to the mobile phase provided an electrospray ionization (ESI)-friendly and "supercharging" reagent without sacrificing chromatographic performance, which can be used to improve peptide and protein identification in large-scale application.

A Targeted LC-MS Strategy for Low-Abundant HLA Class-I-Presented Peptide Detection Identifies Novel Human Papillomavirus T-Cell Epitopes

For rational design of therapeutic vaccines, detailed knowledge about target epitopes that are endogenously processed and truly presented on infected or transformed cells is essential. Many potential target epitopes (viral or mutation-derived), are presented at low abundance. Therefore, direct detection of these peptides remains a challenge. This study presents a method for the isolation and LC-MS3 -based targeted detection of low-abundant human leukocyte antigen (HLA) class-I-presented peptides from transformed cells. Human papillomavirus (HPV) was used as a model system, as the HPV oncoproteins E6 and E7 are attractive therapeutic vaccination targets and expressed in all transformed cells, but present at low abundance due to viral immune evasion mechanisms. The presented approach included preselection of target antigen-derived peptides by in silico predictions and in vitro binding assays. The peptide purification process was tailored to minimize contaminants after immunoprecipitation of HLA-peptide complexes, while keeping high isolation yields of low-abundant target peptides. The subsequent targeted LC-MS3 detection allowed for increased sensitivity, which resulted in successful detection of the known HLA-A2-restricted epitope E711-19 and ten additional E7-derived peptides on the surface of HPV16-transformed cells. T-cell reactivity was shown for all the 11 detected peptides in ELISpot assays, which shows that detection by our approach has high predictive value for immunogenicity. The presented strategy is suitable for validating even low-abundant candidate epitopes to be true immunotherapy targets.

Sensitive quantification of the somatostatin analog AP102 in plasma by ultra-high pressure liquid chromatography-tandem mass spectrometry and application to a pharmacokinetic study in rats

AP102 is a di-iodinated octapeptide somatostatin agonist (SSA) designed to treat acromegaly and neuroendocrine tumors. A sensitive and selective method was validated for the quantification of AP102 in plasma following the European Medicines Agency (EMA) and Food and Drug Administration (FDA) guidelines. Sample preparation was performed using solid-phase extraction microplates. Chromatographic separation was achieved on an ultra-high pressure liquid chromatography (UHPLC) C18 column in 6.0 minutes. The compounds were quantified using multiple reaction monitoring on a tandem quadrupole mass spectrometer with ¹³ C,¹⁵ N-labeled AP102 as internal standard. Calibration ranged from 50 to 10000 pg/mL. The lower limit of quantification (LLOQ) was measured at 20 pg/mL, and robust analytical performances were obtained with trueness at 99.2%-100.0%, intra-assay imprecision at 2.5%-4.4%, and inter-assay imprecision at 8.9%-9.7%. The accuracy profiles (total error) built on the 3 concentrations levels showed accuracy within the 70%-130% range. AP102 is remarkably stable since no proteolytic fragments were detected on plasma samples analyzed by Orbitrap-MS. Pharmacokinetic studies were conducted in rats, after single dose (1, 3, and 10 μg/kg, sc) and continuous subcutaneous administration (osmotic minipumps for 28 days, 3.0 or 10.0 μg/kg/h). AP102 showed a rapid absorption by the subcutaneous route (T_max : 15-30 minutes) and a fast elimination (t_1/2 : 33-86 minutes). The PK profile of AP102 exhibited a mean clearance of 1.67 L/h and a mean distribution volume at steady state of 7.16 L/kg, about 10-fold higher than those observed with other SSA or non- and mono-iodinated AP102. LogD_7.4 determination confirmed the lipophilic properties of AP102 that might influence its distribution in tissues.

Development of Isocratic RP-HPLC Method for Separation and Quantification of L-Citrulline and L-Arginine in Watermelons

Watermelons (Citrullus lanatus) are known to have sufficient amino acid content. In this study, watermelons grown and consumed in Malaysia were investigated for their amino acid content, L-citrulline and L-arginine, by the isocratic RP-HPLC method. Flesh and rind watermelons were juiced, and freeze-dried samples were used for separation and quantification of L-citrulline and L-arginine. Three different mobile phases, 0.7% H₃P0₄, 0.1% H₃P0₄, and 0.7% H₃P0₄ : ACN (90 : 10), were tested on two different columns using Zorbax Eclipse XDB-C₁₈ and Gemini C₁₈ with a flow rate of 0.5 mL/min and a detection wavelength at 195 nm. Efficient separation with reproducible resolution of L-citrulline and L-arginine was achieved using 0.1% H₃P0₄ on the Gemini C₁₈ column. The method was validated and good linearity of L-citrulline and L-arginine was obtained with R² = 0.9956, y = 0.1664x + 2.4142 and R² = 0.9912, y = 0.4100x + 3.4850, respectively. L-citrulline content showed the highest concentration in red watermelon of flesh and rind juice extract (43.81 mg/g and 45.02 mg/g), whereas L-arginine concentration was lower than L-citrulline, ranging from 3.39 to 11.14 mg/g. The isocratic RP-HPLC method with 0.1% H₃P0₄ on the Gemini C₁₈ column proved to be efficient for separation and quantification of L-citrulline and L-arginine in watermelons.

Qualitative analysis of antibody–drug conjugates (ADCs): an experimental comparison of analytical techniques of cysteine-linked ADCs

Four different cysteine linked antibody-drug conjugates (ADCs) consisting of Trastuzumab-vc-MMAE were analysed with four common analytical techniques with respect to drug-to-antibody ratio (DAR) and molecular weight.