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Biological therapeutics are major contributors to the pharmaceutical pipeline and continue to grow in sales and scope. Additionally, the field's understanding of cancer biology has advanced such that biopharmaceuticals can harness the power of the immune system for oncology treatments. Several of these novel therapeutics are engineered versions of naturally occurring proteins designed to improve therapeutic properties including potency, target engagement and half-life extension. Cytokines, such as interferons and interleukins, are a broad class of signaling proteins which modulate the body's immune response; engineered cytokines have entered the clinic as promising new immuno-oncology therapies. While these therapies hold great promise, their additional structural complexity introduces analytical challenges, and traditional analytical platforms may be ill-suited to effectively assess product development risks. Further, the pharmaceutical industry relies on streamlining approaches for high-throughput experimentation to achieve speed and efficiency for the discovery and development of new modalities. These demands necessitate the use of state-of-the-art techniques to rapidly characterize these new modalities and guide process development and optimization. Matrix Assisted Laser Desorption Ionization Mass Spectrometry (MALDI-MS) is a rapid, sensitive and automatable technique amenable for high-throughput analysis of proteins. In this work, we have developed an automated MALDI-MS platform to prepare, acquire and analyze molecular degradation in engineered PEGylated cytokines formulation samples. This orthogonal technique integrated seamlessly with current developability risk assessment workflows, ultimately enabling selection of a final formulation strategy for clinical development., Competing Interests: Declaration of Competing Interests The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 American Pharmacists Association. All rights reserved.)

Peptide therapeutics are a growing modality in the pharmaceutical industry and expanding these therapeutics to hit intracellular targets would require establishing cell permeability. Rapid measurement target-agnostic cell permeability of peptides is still analytically challenging. In this study, we demonstrate the development of a rapid high-throughput label-free methodology based on a MALDI-hydrogen-deuterium exchange mass spectrometry (MALDI-HDX-MS) approach to rank-order peptide cell membrane permeability using live THP-1 and AsPc-1 cells. Peptides were incubated in the presence of live cells and their permeability into the cells over time was measured by MALDI-HDX-MS. A differential hydrogen-deuterium exchange approach was used to distinguish the peptides outside of the cells from those inside. The peptides on the outside of the cells were labeled using sufficiently short exposure to deuterium oxide, while the peptides inside of the cells were protected from labeling as a result of permeation into the cells. The deuterium labeled and peak area ratios of unlabeled peptides were compared and plotted over time. The developed methodology, referred to as Cell-based Approach Membrane Permeability Assay (CAMPA), was applied to study an array of 24 diverse peptides including cell-penetrating peptides, stapled and macrocyclic peptides. The cell membrane permeability results observed by CAMPA were corroborated by previously reported in literature data. The CAMPA MALDI-MS analysis was fully automated including MS data processing using internally developed Python scripts. Moreover, CAMPA was demonstrated to be useful for differentiating passive and active cell transportation by using an endocytosis inhibitor in cell incubation media for selected peptides., (Copyright © 2022 Elsevier B.V. All rights reserved.)

Recent advances in biomedical and pharmaceutical processes has enabled a notable increase of protein- and peptide-based drug therapies and vaccines that often contain a higher-order structure critical to their efficacy. Hyphenation of chromatographic and spectrometric techniques is at the center of all facets of biopharmaceutical analysis, purification and chemical characterization. Although computer-assisted chromatographic modeling of small molecules has reached a mature stage across the pharmaceutical industry, software-based method optimization approaches for large molecules has yet to see the same revitalization. Conformational changes of biomolecules under chromatographic conditions have been identified as the major culprit in terms of sub-optimal modeling outcomes. In order to circumvent these challenges, we herein investigate the outcomes generated via computer-assisted modeling from using different chaotropic and denaturing mobile phases (trifluoroacetic acid, sodium perchlorate and guanidine hydrochloride in acetonitrile/water-based eluents). Linear and polynomial regression retention models using ACD/Labs software were built as a function of gradient slope, column temperature and mobile phase buffer for eight different model proteins ranging from 12 to 670 kDa (holo-transferrin, cytochrome C, apomyoglobin, ribonuclease A, ribonuclease A type I-A, albumin, y-globulin and thyroglobulin bovine). Correlation between experimental and modeled outputs was substantially improved by using strong chaotropic and denaturing modifiers in the mobile phase, even when using linear regression modeling as typically observed for small molecules. On the contrary, the use of conventional TFA buffer concentrations at low column temperatures required the used of polynomial regression modeling indicating potential conformational structure changes of proteins upon chromatographic conditions. In addition, we illustrate the power of modern computer-assisted chromatography modeling combined with chaotropic agents in the developing of new RPLC assays for protein-based therapeutics and vaccines., (Copyright © 2021. Published by Elsevier B.V.)

At the forefront of synthetic endeavors in the pharmaceutical industry, including drug discovery and high-throughput screening, timelines are tight and large quantities of pure chemical targets are rarely available. In this regard, the development of novel and increasingly challenging chemistries requires a commensurate level of innovation to develop reliable analytical assays and purification workflows with rapid turnaround that enables accelerated pharmacological evaluation. A small-scale automation platform enabling high-throughput analysis and purification to streamline the selection of candidate leads would be a transformative advance. Herein, we introduce an automation-friendly solid-phase extraction-matrix-assisted laser desorption/ionization (SPE-MALDI) platform applied to the high-throughput purification and analysis of peptide libraries. This advance enabled us to purify peptides from microgram levels in less than a day with results comparable to traditional high-performance liquid chromatography-diode array detection-mass spectrometry (HPLC-DAD-MS)., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2020 Elsevier B.V. All rights reserved.)

A stereoselective method was developed for the synthesis of synthetic analogues of natural 5Z,9Z-dienoic acids by esterification of aliphatic and aromatic alcohols and carboxylic acids with (5Z,9Z)-1,14-tetradeca-5,9-dienedioic acid and (5Z,9Z)-1,14-tetradeca-5,9-dienediol, synthesized by Ti-catalyzed homo-cyclomagnesiation of the tetrahydropyran ether of hepta-5,6-dien-1-ol with Grignard reagents. In order to establish the effect of molecular structure on the antitumor activity, the obtained 5Z,9Z-dienoic acids were tested for the inhibitory activity against human topoisomerase I, the cytotoxic activity in vitro against several cancer and normal cell lines (Jurkat, HL-60, K562, U937, fibroblasts), the effect on the cell cycle, and apoptosis-inducing ability using flow cytofluorometry. In addition, the effect of the synthesized acids on the cancer cell production of some phosphorylated and unphosphorylated proteins responsible for proliferation and apoptosis was studied by a new multiplex assay technology, MAGPIX., (Copyright © 2020 Elsevier Inc. All rights reserved.)

The pharmaceutical industry's focus has expanded to include peptide and protein-based therapeutics; however, some analytical challenges have arisen along the way, including the urgent need for fast and robust measurement of the membrane permeability of peptides and small proteins. In this study, a simple and efficient approach that utilizes MALDI-TOF-MS to study peptide and protein permeability through an artificial liposome membrane in conjunction with a differential hydrogen-deuterium exchange (HDX) methodology is described. A non-aqueous (aprotic) matrix was evaluated for use with MALDI sample preparation in order to eliminate undesirable hydrogen-deuterium back-exchange. Peptides and proteins were incubated with liposomes and their penetration into the liposome membrane over time was measured by MALDI-MS. A differential HDX approach was used to distinguish the peptides outside of the liposome from those inside. In this regard, the peptides on the outside of the liposomes were labeled using short exposure to deuterium oxide, while the peptides inside of the liposomes were protected from labeling. Subsequently, the unlabeled versus labeled peak area ratios for peptide and protein samples were compared using MALDI-TOF-MS. In this proof-of-concept study, we developed the Liposome Artificial Membrane Permeability Assay (LAMPA) workflow to study three well-known membrane-active model peptides (melittin, alamethicin, and gramicidin) and two model proteins (aprotinin and ubiquitin). The permeability results obtained from this were corroborated by previously reported data for studied peptides and proteins. The proposed LAMPA by MALDI-HDX-MS can be applied in an ultra-high-throughput manner for studying and rank-ordering membrane permeability of peptides and small proteins., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2019 Elsevier B.V. All rights reserved.)

Biological therapeutics are established as major contributors to the pharmaceutical pipeline. Many of these biological drugs are lyophilized to preserve their conformation and reduce decomposition during storage and shipping. Therefore, understanding and controlling the effects of lyophilization on protein higher order structure is critical for commercialization of biologics. Hydrogen Deuterium Exchange Mass Spectrometry (HDX-MS) is a well-established technique for studying protein higher order structure. Previous publications have demonstrated a solid state HDX (ssHDX) method for labeling formulated, lyophilized proteins to assess their physical stability during, but this process still suffered from low throughput and undesired back exchange. Recently, our group described a method combining HDX-MS with MALDI to greatly reduce the time of analysis and nearly eliminate H/D back-exchange, but that method was not suited for interrogating solid samples. This work integrates the two techniques to assess and predict the stability of peptides and proteins following mixing and lyophilization with various excipient formulations. Sample mixing and handling were performed through the use of a bench-top robotics and programmed data MALDI-MS acquisition allowed for monitoring deuterium incorporation for dried peptides and protein samples following continuous labeling with D 2 O vapor. Effects of excipients upon peptide stability were also tracked and compared to a control for a three day labeling time course. This workflow is automated and free from back-exchange. As demonstrated by deuterium retention of bradykinin, these features serve to reduce experimental error normally associated with conventional deuterium exchange experiments. The proposed union of MALDI-MS and ssHDX can be applied to study higher order structure of proteins and peptides and the effects of added excipients in an environment that closely resembles the storage and shipping conditions of biopharmaceuticals and may be beneficial in giving insights studying protein structural dynamics in solids., (Copyright © 2019 Elsevier B.V. All rights reserved.)

Supercritical fluid chromatography (SFC) has become the fastest growing analytical tool for chiral and achiral small-molecule pharmaceutical separations. The benefits from savings in cost (as a result of lower solvent and energy consumption), and time have made SFC a proven effective tool for solving many analytical problems for small-molecules over the years. There is, however, a gap in the application of SFC for larger biomolecules, proteins and peptides. There has been a notable increase of protein- and peptide-based drug therapies that contain a higher-order structure important to their efficacy. These studies leverage the use of size exclusion chromatography coupled with hydrogen-deuterium exchange (SEC-HDX) methodology and circular dichroism (CD) spectroscopy to probe global conformational structures of model peptides and proteins following purification by preparative SFC. It was demonstrated that bradykinin and insulin can be used in SFC purification, and moreover, insulin was able to recover its original higher-order structure when compared to pre-purification insulin by three orthogonal techniques: 1) calculated percent alpha-helicity based on CD spectra, 2) alpha-helix - temperature hysteresis analysis by CD and 3) SEC-HDX-MS at different temperatures. However, it was shown that the higher order structures of the other three model proteins used in the study (ubiquitin, cytochrome C, and apomyoglobin) were significantly modified during SFC purification and were unable to re-fold to their original conformations. The present workflow was applied successfully to several peptide therapeutic programs at our comp any and in addition can be applied for small proteins., (Copyright © 2019 Elsevier B.V. All rights reserved.)

Misfolding of therapeutic peptides and proteins can lead to numerous issues, ranging in severity, including loss of function, aggregation, immunogenicity, and cytotoxicity. A primary component of protein folding is secondary structure, including α-helices and β-sheets. Many native peptides and proteins are predominately α-helical therefore, it is of critical importance to develop robust and reliable analytical tools to investigate protein higher order structure, including the percentage of α-helix under various conditions, to evaluate protein folding and prevent the negative effects of misfolding. However, given the complexity of protein folding and higher order structure, it is unlikely that one technique will provide a comprehensive analysis. To bridge this gap, this study presents the combination of two orthogonal techniques - circular dichroism (CD) and size-exclusion chromatography-hydrogen-deuterium exchange-mass spectrometry (SEC-HDX-MS) to investigate global peptide and protein conformations. Also, the incorporation of trifluoroethanol (TFE), a known stabilizer of α-helical structures, into the analyses, aims to enhance the discrimination power of these two techniques by increasing the alpha helical stability range of study. CD data was used to estimate the percent of α-helix content and its thermal stability while online SEC-HDX-MS screening compared global conformational changes of each peptide based on a difference in the number of deuterons exchanged to protons, ΔHDX. The workflow described in this report can be very beneficial in pharmaceutical development. The model peptides were chosen to demonstrate the workflow with commercially available compounds. The goal of this study was to show a proof-of-concept for direct correlation of these methodologies and to estimate the percentage of α-helix content at a particular ΔHDX, which is indicative of the state of protein folding., (Copyright © 2018. Published by Elsevier B.V.)

Nucleotides are among the most frequently used chemical building blocks in the research, development and manufacture of drug substances. They are composed of three highly polar subunit molecules (a nucleobase, a sugar, and at least one phosphate group), which makes their separation and analysis very challenging by conventional liquid chromatography techniques. Herein, we describe a simple, efficient, and cost-effective ion-exchange chromatography (IEC) method for the separation and purification of over 20 nucleotides. This method combines the use of a Tosoh TSKgel SuperQ-5P W resin in conjunction with a fully aqueous eluent profile (ammonium bicarbonate-based) that allows for a straightforward scale-up transition and convenient drying process with minimal environmental impact. This generic method was optimized using chromatography simulation software (ACD Labs/LC Simulator) and successfully applied to the preparative purification of multicomponent nucleotide mixtures using readily available Fast Protein Liquid Chromatography (FPLC) instrumentation. These IEC method conditions can be effectively applied as the starting point for method development and isolation of other highly polar nucleotide species beyond those investigated in this study., (Copyright © 2018 Elsevier B.V. All rights reserved.)

Column temperature control is a fundamental component of liquid chromatography experiments. However, it is typically monitored indirectly by tracking the temperature of an adjacent heating element that exchanges heat with the column in a controlled environment. The practice of not directly measuring the column temperature means that uncontrolled contributions of heat, such as frictional heating inside the column, can be overlooked. The present work describes the use of a high-resolution infrared thermal imaging camera to directly measure the column heat map during mobile phase flow. The approach was used to measure the longitudinal temperature gradient formed with three common mobile phases: water, methanol, and acetonitrile, in two 50 mm reversed-phase columns, a 1.7 μm particle-packed column and a polystyrene divinylbenzene monolith. In a close approximation to an adiabatic environment, the temperature gradients (ΔT) observed with the 1.7 μm particle column at a linear velocity of 5.8 mm/s were up to +16.6 and + 12.8 °C above an ambient temperature of 23 °C for water and acetonitrile, respectively. In the case of water, the measured temperature gradient values (ΔT) were within 1% difference of theoretically-calculated values and on average within 10% for acetonitrile. By contrast, the ΔT observed in the monolith was negligible. The elevated temperatures that are generated through friction in sub-2 μm particle columns may be particularly important to consider for the design of experiments that measure structural features of temperature-sensitive analytes, such as biomolecules. While frictional heating is one important application of the thermal imaging approach described, the technique can be used to provide a data-rich profile of heat exchange in numerous experimental configurations, chromatographic or otherwise., (Copyright © 2018 Elsevier B.V. All rights reserved.)

Impurity fate and purge studies are critical in order to establish an effective impurity control strategy for approval of the commercial filing application of new medicines. Reversed phase liquid chromatography-diode array-mass spectrometry (RPLC-DAD-MS) has traditionally been the preferred tool for impurity fate mapping. However, separation of some reaction mixtures by LC can be very problematic requiring combination LC-UV for area % analysis and a different LC-MS method for peak identification. In addition, some synthetic intermediates might be chemically susceptible to the aqueous conditions used in RPLC separations. In this study, the use of supercritical fluid chromatography-photodiode array-electrospray ionization mass spectrometry (SFC-PDA-ESIMS) for fate and purge of two specified impurities in the 1-uridine starting material from the synthesis of a bis-piv 2'keto-uridine, an intermediate in the synthesis of uprifosbuvir, a treatment under investigation for chronic hepatitis C infection. Readily available SFC instrumentation with a Chiralpak IC column (4.6 × 150 mm, 3 μm) and ethanol: carbon dioxide based mobile phase eluent enabled the separation of closely related components from complex reaction mixtures where RLPC failed to deliver optimal chromatographic performance. These results illustrate how SFC combined with PDA and ESI-MS detection can become a powerful tool for direct impurity fate mapping across multiple reaction steps., (Copyright © 2018 Elsevier B.V. All rights reserved.)

Verubecestat is an inhibitor of β-site amyloid precursor protein cleaving enzyme 1 (BACE1) being evaluated in clinical trials for the treatment of Alzheimer's disease. Synthetic route development involves diastereoselective transformations with a need for enantiomeric excess (ee) determination of each intermediate and final active pharmaceutical ingredient (API). The analytical technical package of validated methods relies on enantioselective SFC and RPLC separations using multiple 3 and 5 μm coated polysaccharide-based chiral stationary phases (CSPs) and mobile phases combinations. Evaluation of recently developed chiral columns revealed a single chiral selector (Teicoplanin) bonded to 2.7 μm core-shell particles using H 3 PO 4 in H 2 O/ACN and triethylammonium acetate: methanol based eluents at different isocratic compositions allowed good enatioseparation of all verubecestat intermediates. EE determination of verubecestat is easily performed on NicoShell, another macrocyclic glycopeptide chiral selector bonded to 2.7 μm superficially porous particles. This approach enables fast and reliable enantiopurity analysis of the entire verubecestat synthetic route using only two chiral columns and mobile phases on a conventional HPLC system, simplifying technical package preparation, method validation and transfer to manufacturing facilities., (Copyright © 2018 Elsevier B.V. All rights reserved.)

Development of methodologies for studying protein higher-order structure in solution helps to establish a better understanding of the intrinsic link between protein conformational structure and biological function and activity. The goal of this study was to demonstrate a simultaneous screening approach for global protein conformational changes in solution through the combination of ion mobility spectrometry-mass spectrometry (IMS-MS) with differential hydrogen-deuterium exchange (ΔHDX) on the size-exclusion chromatography (SEC) platform in a single on-line workflow. A semi-automated experimental setup based on the use of SEC on-column conditions allowed for tracking of protein conformational changes in solution as a function of acetonitrile concentration. In this setup, the SEC protein elution data was complemented by the ΔHDX profile which showed global protein conformational changes as a difference in the number of deuterons exchanged to protons. The ΔHDX data, in turn, was complemented by the changes in the drift time by IMS-MS. All three orthogonal techniques were applied for studying global higher-order structure of the proteins ubiquitin, cytochrome c and myoglobin, in solution simultaneously. The described approach allows for the use of a crude sample (or mixture of proteins) and could be suitable for rapid comparison of protein batch-to-batch higher-order structure or for optimizing conditions for enzymatic reactions., (Copyright © 2017 Elsevier B.V. All rights reserved.)

Pressure is not typically controlled or adjusted independently of flow rate during method development in reversed-phase LC (RPLC). However, it has been shown that pressure has an effect on analyte molecular molar volume, and the magnitude of this effect is greater for proteins and ionizable compounds than neutral small molecules. This phenomenon has received attention recently in the context of porous sub-2-micron particle packed columns. The present study surveys the effect of pressure and frictional heating on RPLC separations using commercially-available monolithic columns at constant flow rate and with controlled external temperature. Because the current monoliths cannot be operated at high pressures, all experiments were conducted with pressures at or below 200bar. Nonetheless, substantial changes in retention were still observed; for example, an increase in pressure of 75bar shifted the retention factor for bovine insulin from 1.27 to 1.78, a 40% increase, while a similar experiment with the neutral small molecule, toluene, showed no change in retention. Results are presented from investigations of model peptides and proteins ranging in size from 1kDa to 30kDa, as well as experiments performed with a silica-based C18 monolith and a polystyrene divinylbenzene monolith functionalized with a phenyl stationary phase. This work indicates that protein separations in monoliths are highly pressure sensitive, and pressure should therefore be considered as an additional parameter in method development for optimizing retention and selectivity. Given these findings, and the ever-increasing importance of chromatographic separations of proteins in both industrial and academic laboratories, improved instrumentation and mechanisms for directly controlling system backpressure could be of great practical value., (Copyright © 2017 Elsevier B.V. All rights reserved.)

Methods for protein characterization are being actively developed based on the growing importance of protein therapies and applications. The goal of this study was to demonstrate the use of size-exclusion chromatography (SEC) in combination with differential hydrogen-deuterium exchange (HDX) to compare protein global conformational changes at different solution conditions. Using chaotropic mobile phase additive, differential HDX was used to detect a number of solvent accessible labile protons of protein on-column at pH and temperature conditions which provided unrestricted intrinsic H/D exchange (all-or-nothing approach). Varying SEC on-column conditions allowed for protein conformational changes to be observed. Temperature and pressure were independently studied with regards to their effect on the proteins' (insulin, cytochrome C, ubiquitin, and myoglobin) conformational changes in the solution. The obtained ΔHDX profiles revealed protein conformational changes in solution under varied conditions manifested as the difference in the number of protons exchanged to deuterons, or vice-versa. The approach described in this manuscript could prove useful for protein batch-to-batch comparisons, for optimization of chemical reactions with enzyme as catalyst or for protein chemical modification reactions., (Copyright © 2016 Elsevier B.V. All rights reserved.)

Evaluation of a several fluorine-containing stationary phases for the chromatographic separation of fluorine-containing pharmaceuticals from their corresponding desfluoro analogs revealed a number of perfluoroaryl and perfluoroalky stationary phases that afford good separations. These fluorous stationary phases exhibit greater retention for the fluorine-containing compounds relative to the H-containing analogs, consistent with a fluorophilic retention mechanism. While both perfluoroalkyl and perfluoroaryl stationary phases afford adequate resolution, the perfluoroaryl columns generally exhibit superior separation factor (α) and peak efficiency (N), resulting in faster baseline separations, with the Hypersil Gold PFP and Poroshell 120 PFP columns providing the best overall performance for the test group studied., (Copyright © 2014 Elsevier B.V. All rights reserved.)

Commercially available ultra high pressure liquid chromatography (UHPLC) equipment offers the ability to explore the influence of backpressure on chromatographic separations. However, the influence of pressure on the chromatographic separation of enantiomers on chiral stationary phases remains largely unexplored. In this investigation we surveyed the effects of pressure on the separation of enantiomers using several reversed-phase chiral stationary phases. The experiments were conducted at constant flow rate and column temperature, using isocratic conditions. The only variable parameter was pressure, which was adjusted using a post-column backpressure regulator. For the separation of enantiomers on chiral stationary phases, an increase in pressure from approximately 2,000 psi (138 bar) to approximately 8,000 psi (552 bar) at constant flow rate and temperature led to an increase of retention factors for some analytes and a decrease for others. Achiral separations on a C-18 stationary phase always led only to an increase of retention factor. Interestingly, changes in pressure led to small changes in enantioselectivity during reversed-phase chiral separation of enantiomers, suggesting that such studies may be of value for better understanding the mechanisms underlying chromatographic enantioseparation., (Copyright © 2014 Elsevier B.V. All rights reserved.)