Biosensor-Enabled Deconvolution of the Avidity-Induced Affinity Enhancement for the SARS-CoV-2 Spike Protein and ACE2 Interaction.

Avidity is an effective and frequent phenomenon employed by nature to achieve extremely high-affinity interactions. As more drug discovery efforts aim to disrupt protein-protein interactions, it is becoming increasingly common to encounter systems that utilize avidity effects and to study these systems using surface-based technologies, such as surface plasmon resonance (SPR) or biolayer interferometry. However, heterogeneity introduced from multivalent binding interactions complicates the analysis of the resulting sensorgram. A frequently applied practice is to fit the data based on a 1:1 binding model, and if the fit does not describe the data adequately, then the experimental setup is changed to favor a 1:1 binding interaction. This reductionistic approach is informative but not always biologically relevant. Therefore, we aimed to develop an SPR-based assay that would reduce the heterogeneity to enable the determination of the kinetic rate constants for multivalent binding interactions using the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein and the human receptor angiotensin-converting enzyme 2 (ACE2) as a model system. We employed a combinatorial approach to generate a sensor surface that could distinguish between monovalent and multivalent interactions. Using advanced data analysis algorithms to analyze the resulting sensorgrams, we found that controlling the surface heterogeneity enabled the deconvolution of the avidity-induced affinity enhancement for the SARS-CoV-2 spike protein and ACE2 interaction.

A Retention-Matching Strategy for Method Transfer in Supercritical Fluid Chromatography: Introducing the Isomolar Plot Approach.

A strategy to match any retention shifts due to increased or decreased pressure drop during supercritical fluid chromatography (SFC) method transfer is presented. The strategy relies on adjusting the co-solvent molarity without the need to adjust the back-pressure regulator. Exact matching can be obtained with minimal changes in separation selectivity. To accomplish this, we introduce the isomolar plot approach, which shows the variation in molar co-solvent concentration depending on the mass fraction of co-solvent, pressure, and temperature, here exemplified by CO2-methanol. This plot allowed us to unify the effects of the co-solvent mass fraction and density on retention in SFC. The approach, which was verified on 12 known empirical retention models for each enantiomer of six basic pharmaceuticals, allowed us to numerically calculate the apparent retention factor for any column pressure drop. The strategy can be implemented either using a mechanistic approach if retention models are known or empirically by iteratively adjusting the co-solvent mass fraction. As a rule of thumb for the empirical approach, we found that the relative mass fraction adjustment needed is proportional to the relative change in the retention factor caused by a change in the pressure drop. Different proportionality constants were required to match retention in the case of increasing or decreasing pressure drops.

Advanced Analysis of Biosensor Data for SARS-CoV-2 RBD and ACE2 Interactions.

The traditional approach for analyzing interaction data from biosensors instruments is based on the simplified assumption that also larger biomolecules interactions are homogeneous. It was recently reported that the human receptor angiotensin-converting enzyme 2 (ACE2) plays a key role for capturing SARS-CoV-2 into the human target body, and binding studies were performed using biosensors techniques based on surface plasmon resonance and bio-layer interferometry. The published affinity constants for the interactions, derived using the traditional approach, described a single interaction between ACE2 and the SARS-CoV-2 receptor binding domain (RBD). We reanalyzed these data sets using our advanced four-step approach based on an adaptive interaction distribution algorithm (AIDA) that accounts for the great complexity of larger biomolecules and gives a two-dimensional distribution of association and dissociation rate constants. Our results showed that in both cases the standard assumption about a single interaction was erroneous, and in one of the cases, the value of the affinity constant KD differed more than 300% between the reported value and our calculation. This information can prove very useful in providing mechanistic information and insights about the mechanism of interactions between ACE2 and SARS-CoV-2 RBD or similar systems.

Impact of Methanol Adsorption on the Robustness of Analytical Supercritical Fluid Chromatography in Transfer from SFC to UHPSFC.

In supercritical fluid chromatography (SFC), the retention of a solute depends on the temperature, density, pressure, and cosolvent fraction. Here, we investigate how the adsorption of the cosolvent MeOH changes with pressure and temperature and how this affects the retention of several solutes. The lower the pressure, the stronger the MeOH adsorption to the stationary phase; in addition, at low pressure, perturbing the pressure results in significant changes in the amounts of MeOH adsorbed to the stationary phase. The robustness of the solute retention was lowest when operating the systems at low pressures, high temperatures, and low cosolvent fractions in the eluent. Here, we found a clear relationship between the sensitivity of MeOH adsorption to the stationary phase and the robustness of the separation system. Finally, we show that going from classical SFC to ultrahigh-performance SFC (UHPSFC), that is, separations conducted with much smaller packing diameters, results in retention factors that are more sensitive to fluctuations in the flow rate than with traditional SFC. The calculated density profiles indicate only a slight density drop over the traditional SFC column (3%, visualized as lighter → darker blue in the TOC), whereas the drop for the UHPSFC one was considerably larger (20%, visualized as dark red → light green in the TOC). The corresponding temperature drops were calculated to be 0.8 and 6.5 °C for the SFC and UHPSFC systems, respectively. These increased density and temperature drops are the underlying reasons for the decreased robustness of UHPSFC.

Analytical and preparative separation of phosphorothioated oligonucleotides: columns and ion-pair reagents.

Oligonucleotide drugs represent an emerging area in the pharmaceutical industry. Solid-phase synthesis generates many structurally closely related impurities, making efficient separation systems for purification and analysis a key challenge during pharmaceutical drug development. To increase the fundamental understanding of the important preparative separation step, mass-overloaded injections of a fully phosphorothioated 16mer, i.e., deoxythymidine oligonucleotide, were performed on a C18 and a phenyl column. The narrowest elution profiles were obtained using the phenyl column, and the 16mer could be collected with high purity and yield on both columns. The most likely contribution to the successful purification was the quantifiable displacement of the early-eluting shortmers on both columns. In addition, the phenyl column displayed better separation of later-eluting impurities, such as the 17mer impurity. The mass-overloaded injections resulted in classical Langmuirian elution profiles on all columns, provided the concentration of the ion-pairing reagent in the eluent was sufficiently high. Two additional column chemistries, C4 and C8, were also investigated in terms of their selectivity and elution profile characteristics for the separation of 5-20mers fully phosphorothioated deoxythymidine oligonucleotides. When using triethylamine as ion-pairing reagent to separate phosphorothioated oligonucleotides, we observed peak broadening caused by the partial separation of diastereomers, predominantly seen on the C4 and C18 columns. When using the ion-pair reagent tributylamine, to suppress diastereomer separation, the greatest selectivity was found using the phenyl column followed by C18. The present results will be useful when designing and optimizing efficient preparative separations of synthetic oligonucleotides.

Investigation of factors influencing the separation of diastereomers of phosphorothioated oligonucleotides.

This study presents a systematic investigation of factors influencing the chromatographic separation of diastereomers of phosphorothioated pentameric oligonucleotides as model solutes. Separation was carried out under ion-pairing conditions using an XBridge C18 column. For oligonucleotides with a single sulfur substitution, the diastereomer selectivity was found to increase with decreasing carbon chain length of the tertiary alkylamine used as an ion-pair reagent. Using an ion-pair reagent with high selectivity for diastereomers, triethylammonium, it was found the selectivity increased with decreased ion-pair concentration and shallower gradient slope. Selectivity was also demonstrated to be dependent on the position of the modified linkage. Substitutions at the center of the pentamer resulted in higher diastereomer selectivity compared to substitutions at either end. For mono-substituted oligonucleotides, the retention order and stereo configuration were consistently found to be correlated, with Rp followed by Sp, regardless of which linkage was modified. The type of nucleobase greatly affects the observed selectivity. A pentamer of cytosine has about twice the diastereomer selectivity of that of thymine. When investigating the retention of various oligonucleotides eluted using tributylammonium as the ion-pairing reagent, no diastereomer selectivity could be observed. However, retention was found to be dependent on both the degree and position of sulfur substitution as well as on the nucleobase. When analyzing fractions collected in the front and tail of overloaded injections, a significant difference was found in the ratio between Rp and Sp diastereomers, indicating that the peak broadening observed when using tributylammonium could be explained by partial diastereomer separation.

Reliable Strategy for Analysis of Complex Biosensor Data.

When using biosensors, analyte biomolecules of several different concentrations are percolated over a chip with immobilized ligand molecules that form complexes with analytes. However, in many cases of biological interest, e.g., in antibody interactions, complex formation steady-state is not reached. The data measured are so-called sensorgram, one for each analyte concentration, with total complex concentration vs time. Here we present a new four-step strategy for more reliable processing of this complex kinetic binding data and compare it with the standard global fitting procedure. In our strategy, we first calculate a dissociation graph to reveal if there are any heterogeneous interactions. Thereafter, a new numerical algorithm, AIDA, is used to get the number of different complex formation reactions for each analyte concentration level. This information is then used to estimate the corresponding complex formation rate constants by fitting to the measured sensorgram one by one. Finally, all estimated rate constants are plotted and clustered, where each cluster represents a complex formation. Synthetic and experimental data obtained from three different QCM biosensor experimental systems having fast (close to steady-state), moderate, and slow kinetics (far from steady-state) were evaluated using the four-step strategy and standard global fitting. The new strategy allowed us to more reliably estimate the number of different complex formations, especially for cases of complex and slow dissociation kinetics. Moreover, the new strategy proved to be more robust as it enables one to handle system drift, i.e., data from biosensor chips that deteriorate over time.

Impact of column and stationary phase properties on the productivity in chiral preparative LC.

By generating 1500 random chiral separation systems, assuming two-site Langmuir interactions, we investigated numerically how the maximal productivity (PR,max ) was affected by changes in stationary phase adsorption properties. The relative change in PR,max , when one adsorption property changed 10%, was determined for each system and for each studied parameter the corresponding productivity change distribution of the systems was analyzed. We could conclude that there is no reason to have columns with more than 500 theoretical plates and larger selectivity than 3. More specifically, we found that changes in selectivity have a major impact on PR,max if it is below ∼2 and, interestingly, increasing selectivity when it is above ∼3 decreases PR,max . Increase in relative saturation capacity will have a major impact on PR,max if it is below ∼40%, but only modest above this percent. Increasing total monolayer saturation capacity, or decreasing the first eluting enantiomer's retention factor, will have a modest effect on PR,max and increased efficiency will have almost no effect at all on PR,max unless it is below ∼500 theoretical plates. Finally, we showed that chiral columns with superior analytic performance might have inferior preparative performance, or vice versa. It is, therefore, not possible to assess columns based on their analytical performance alone.

Thermodynamic and kinetic approaches for evaluation of monoclonal antibody - Lipoprotein interactions.

Two complementary instrumental techniques were used, and the data generated was processed with advanced numerical tools to investigate the interactions between anti-human apoB-100 monoclonal antibody (anti-apoB-100 Mab) and apoB-100 containing lipoproteins. Partial Filling Affinity Capillary Electrophoresis (PF-ACE) combined with Adsorption Energy Distribution (AED) calculations provided information on the heterogeneity of the interactions without any a priori model assumptions. The AED calculations evidenced a homogenous binding site distribution for the interactions. Quartz Crystal Microbalance (QCM) studies were used to evaluate thermodynamics and kinetics of the Low-Density Lipoprotein (LDL) and anti-apoB-100 Mab interactions. High affinity and selectivity were observed, and the emerging data sets were analysed with so called Interaction Maps. In thermodynamic studies, the interaction between LDL and anti-apoB-100 Mab was found to be predominantly enthalpy driven. Both techniques were also used to study antibody interactions with Intermediate-Density (IDL) and Very Low-Density (VLDL) Lipoproteins. By screening affinity constants for IDL-VLDL sample in a single injection we were able to distinguish affinity constants for both subpopulations using the numerical Interaction Map tool.

Estimation of Nonlinear Adsorption Isotherms in Gradient Elution RP-LC of Peptides in the Presence of an Adsorbing Additive.

ABSTRACT: In electrostatic repulsive interaction chromatography, using a charged surface hybrid sorbent carrying positive charges can improve the peak shape of peptides in reversed-phase liquid chromatography (RP-LC), especially in overloaded conditions, compared with standard C18 sorbents. However, the positive surface charges can interact with anionic additives commonly used in peptide separations, e.g., trifluoroacetic acid (TFA), complicating adsorption isotherm estimation. We investigated how the competition for available adsorption sites between TFA and two peptides influenced the adsorption isotherm in gradient elution. A model accounting for the competition with TFA was compared with a model neglecting TFA adsorption. We found that the two models predicted elution profiles with the same accuracy. We also found that the adsorption isotherms were extremely similar in shape, leading to the conclusion that neglecting the competition with TFA is a valid approximation enabling faster and more robust adsorption isotherm estimation for the studied type of sorbent.

Combining Chemometric Models with Adsorption Isotherm Measurements to Study Omeprazole in RP-LC.

The adsorption of the proton-pump inhibitor omeprazole was investigated using RP-LC with chemometric models combined with adsorption isotherm modelling to study the effect of pH and type of organic modifier (i.e., acetonitrile or methanol). The chemometric approach revealed that omeprazole was tailing with methanol and fronting with acetonitrile along with increased fronting at higher pH. The increased fronting with higher pH for acetonitrile was explored using a pH-dependent adsorption isotherm model that was determined using the inverse method and it agreed well with the experimental data. The model indicated that the peaks exhibit more fronting at high pH due to a larger fraction of charged omeprazole molecules. This model could accurately predict the shape of elution profiles at arbitrary pH levels in the studied interval. Using a two-layer adsorption isotherm model, the difference between acetonitrile and methanol was studied at the lowest pH at which almost all omeprazole molecules are neutral. Omeprazole had adsorbate-adsorbate interactions that were similar in strength for the acetonitrile and methanol mobile phases, while the solute-adsorbent interactions were almost twice as strong with methanol. The difference in the relative strengths of these two interactions likely explains the different peak asymmetries (i.e., tailing/fronting) in methanol and acetonitrile. In conclusion, thermodynamic modelling can complement chemometric modeling in HPLC method development and increase the understanding of the separation.

Choice of Model for Estimation of Adsorption Isotherm Parameters in Gradient Elution Preparative Liquid Chromatography.

The inverse method is a numerical method for fast estimation of adsorption isotherm parameters directly from a few overloaded elution profiles and it was recently extended to adsorption isotherm acquisition in gradient elution conditions. However, the inverse method in gradient elution is cumbersome due to the complex adsorption isotherm models found in gradient elution. In this case, physicochemically correct adsorption models have very long calculation times. The aim of this study is to investigate the possibility of using a less complex adsorption isotherm model, with fewer adjustable parameters, but with preserved/acceptable predictive abilities. We found that equal or better agreement between experimental and predicted elution profiles could be achieved with less complex models. By being able to select a model with fewer adjustable parameters, the calculation times can be reduced by at least a factor of 10.

Partial-filling affinity capillary electrophoresis and quartz crystal microbalance with adsorption energy distribution calculations in the study of biomolecular interactions with apolipoprotein E as interaction partner.

Adsorption energy distribution (AED) calculations were successfully applied to partial-filling affinity capillary electrophoresis (PF-ACE) to facilitate more detailed studies of biomolecular interactions. PF-ACE with AED calculations was employed to study the interactions between two isoforms of apolipoprotein E (apoE) and dermatan sulfate (DS), and a quartz crystal microbalance (QCM) was used in combination with AED calculations to examine the interactions of the 15-amino-acid peptide fragment of apoE with DS. The heterogeneity of the interactions was elucidated. Microscale thermophoresis was used to validate the results. The interactions studied are of interest because, in vivo, apolipoprotein E localizes on DS-containing regions in the extracellular matrix of human vascular subendothelium. Two-site binding was demonstrated for the isoform apoE3 and DS, but only one-site binding for apoE2-DS. Comparable affinity constants were obtained for the apoE2-DS, apoE3-D3, and 15-amino-acid peptide of apoE-DS using the three techniques. The results show that combining AED calculations with modern biosensing techniques can open up another dimension in studies on the heterogeneity and affinity constants of biological molecules.

Regeneration of a silica monolithic rod column using harsh methods followed by firm thermodynamic and kinetic validation.

In this study, a numerical tool is introduced--based on thermodynamic and kinetic separation theory--for validating the regeneration of monolithic rod columns after cutting their inlet sections. A long-used RP-18e monolithic column was deemed to be unfit for further coffee analysis because of poor separation performance. The columns brownish inlet section was physically removed with a lathe, leaving a clean white inlet section. The original and regenerated columns were extensively analyzed and compared using numerical tools for processing adsorption data. The perturbation peak method was used to measure the adsorption isotherm of phenol on the original and regenerated monolith and the adsorption energy distributions were calculated for identifying any change in the degree of heterogeneity. Although peak shapes improved considerably after regeneration, no significant differences were found in the detailed characterization of the processed adsorption data between the original column and the regenerated one. This indicates that the removal of a section of the monolithic bed can be undertaken without damaging the column and columns in which their inlet head sections are contaminated may still function with normal adsorption behavior. In addition, the combined thermodynamic and kinetic methodology could accurately be used to evaluate any regeneration method of columns.

Prediction of overloaded concentration profiles under ultra-high-pressure liquid chromatographic conditions.

In this study, overloaded elution profiles under ultra-high-pressure liquid chromatographic (UHPLC) conditions and accounting for the severe pressure and temperature gradients generated, are compared with experimental data. The model system consisted of an C18 column packed with 1.7-µm particles (i.e., a UHPLC column) and the solute was 1,3,5-tri­tert-butylbenzene eluted with a mobile phase composed of 85/15 (v/v) acetonitrile/water. Two thermal modes were considered, and the solute was eluted at the very high inlet pressures necessary to achieve a highly efficient and rapid chromatographic process, as provided by using columns packed with small particles. However, the high inlet pressure and high linear velocity of the mobile phase caused the production of a significant amount of heat, and consequently, the formation of axial and radial temperature gradients. Due to these gradients, the retention and the mobile phase velocity were no longer constant. Thus, simple mathematical models consisting only of the mass balance equations are unsuitable to properly model the elution profiles. Here, the elution concentration profiles were predicted using a combined two-dimensional heat and mass transfer model, also including the calculation of the mobile phase velocity distribution. The isotherm adsorption model was the bi-Langmuir isotherm model with Henry constants that depended on the local temperature and pressure in the column. These adjustments allowed us to precisely account for changes in the shape and retention of the overloaded concentration profiles in the mobile phase. The proposed model provided accurate predictions of the overloaded concentration profiles, demonstrating good agreement with experimental profiles eluted under severe pressure and temperature gradients in the column even in the most extreme cases where the pressure drops reached 846 bar and the temperature gradients equaled 0.15 K mm-1 and 0.95 K mm-1 in the axial and the radial directions, respectively. In such cases 36 % decrease of the retention factor was observed along the column and 2 % increase in radial direction. These changes, combined with the velocity distribution, shifted the overloaded elution profile's shock towards the center of the column, advancing approximately 3 mm from its initial position close to the column wall. Ultimately, this resulted in the broadening of the elution band.

Three complementary techniques for the clarification of temperature effect on low-density lipoprotein-chondroitin-6-sulfate interaction.

A rigorous processing of adsorption data from quartz crystal microbalance technology was successfully combined with the data obtained by partial filling affinity capillary electrophoresis and molecular dynamics for the clarification of the temperature effect on the interaction of a major glycosaminoglycan chain chondroitin-6-sulfate (C6S) of proteoglycans with low-density lipoprotein (LDL) and with a peptide fragment of apolipoprotein B-100 (residues 3359-3377 of LDL, PPBS). Two experimental techniques and computational atomistic methods demonstrated a nonlinear pattern of the affinity of C6S at temperatures above 38.0 °C to both LDL and PPBS. The temperature affects the interaction of C6S with LDL and PPBS by influencing the structural behavior of glycosaminoglycan C6S and/or that of LDL.

Sample conditions to avoid pH distortion in RP-LC.

Band deformations might take place for acids and bases in preparative applications and adsorption studies where it is necessary to use overloaded injections. In this study, we focus on how deformations can be prevented without using highly concentrated buffers that may precipitate in the eluent. We have systematically investigated how the elution zones depend on which protolytic form the analyte has when it is dissolved. Basic and acidic model compounds are investigated using eluents with different pH values and the resulting elution profiles are compared when the analytes are dissolved in their protonated and deprotonated form, i.e., in uncharged form or as different kinds of salts. Depending on the analyte's protolytic form, a sample zone is created at the column inlet whose pH deviates, more or less, from the bulk eluent's. If the local adsorption strength in this sample zone is greater than the bulk eluent's, the elution profiles are compressed. Under opposite conditions, the eluted bands are more or less deformed and may even be split; completely different deformations can even take place for different kinds of salt combinations. Explanations of these, and other, effects, together with detailed guidelines for proper sample preparation to avoid peak deformations, are given.

Evaluation of a combined linear-nonlinear approach for column characterization using modern alkaline-stable columns as model.

This study investigates if deeper understanding is achieved when combining nonlinear and linear chromatographic column characterization methods. As test systems, two hybrid columns (Phenomenex Gemini-NX C18 and Kromasil Eternity C18) and one classic one (Kromasil-C18) were selected. The nonlinear methods were based on firm adsorption theory and involved determination of adsorption isotherms followed by calculations with a new numerical tool, adsorption energy distribution, on probe components at different pH values. The linear methods involved the hydrophobic subtraction model and selected probe components retention factors as a function of pH. The combined analysis indicated that both complementary and confirmative information can be achieved regarding the actual model systems.

Development of a unified gradient theory for ion-pair chromatography using oligonucleotide separations as a model case.

Ion-pair chromatography is the de facto standard for separating oligonucleotides and related impurities, particularly for analysis but also often for small-scale purification. Currently, there is limited understanding of the quantitative modeling of both analytical and overloaded elution profiles obtained during gradient elution in ion-pair chromatography. Here we will investigate a recently introduced gradient mode, the so-called ion-pairing reagent gradient mode, for both analytical and overloaded separations of oligonucleotides. The first part of the study demonstrates how the electrostatic theory of ion-pair chromatography can be applied for modeling gradient elution of oligonucleotides. When the ion-pair gradient mode is used in a region where the electrostatic surface potential can be linearized, a closed-form expression of retention time can be derived. A unified retention model was then derived, applicable for both ion-pair reagent gradient mode as well as co-solvent gradient mode. The model was verified for two different experimental systems and homo- and heteromeric oligonucleotides of different lengths. Quantitative modeling of overloaded chromatography using the ion-pairing reagent gradient mode was also investigated. Firstly, a unified adsorption isotherm model was developed for both gradient modes. Then, adsorption isotherms parameter of a model oligonucleotide and two major synthetic impurities were estimated using the inverse method. Secondly, the parameters of the adsorption isotherm were then used to investigate how the productivity of oligonucleotide varies with injection volume, gradient slope, and initial retention factor. Here, the productivity increased when using a shallow gradient slope combined with a low initial retention factor. Finally, experiments were conducted to confirming some of the model predictions. Comparison with the conventional co-solvent gradient mode showed that the ion-pairing reagent gradient leads to both higher yield and productivity while consuming less co-solvent.

Strategies for predictive modeling of overloaded oligonucleotide elution profiles in ion-pair chromatography.

Due to their potential for gene regulation, oligonucleotides have moved into focus as one of the preferred modalities modulating currently undruggable disease-associated targets. In the course of synthesis and storage of oligonucleotides a significant number of compound-related impurities can be generated. Purification protocols and analytical methods have become crucial for the therapeutic application of any oligonucleotides, be they antisense oligonucleotides (ASOs), small interfering ribonucleic acids (siRNAs) or conjugates. Ion-pair chromatography is currently the standard method for separating and analyzing therapeutic oligonucleotides. Although mathematical modeling can improve the accuracy and efficiency of ion-pair chromatography, its application remains challenging. Simple models may not be suitable to treat advanced single molecules, while complex models are still inefficient for industrial oligonucleotide optimization processes. Therefore, fundamental research to improve the accuracy and simplicity of mathematical models in ion-pair chromatography is still a necessity. In this study, we predict overloaded concentration profiles of oligonucleotides in ion-pair chromatography and compare relatively simple and more advanced predictive models. The experimental system consists of a traditional C18 column using (dibutyl)amine as the ion-pair reagent and acetonitrile as organic modifier. The models were built and tested based on three crude 16-mer oligonucleotides with varying degrees of phosphorothioation, as well as their respective n - 1 and (P = O)1 impurities. In short, the proposed models were suitable to predict the overloaded concentration profiles for different slopes of the organic modifier gradient and column load.