Ligand Screening of Membrane Proteins Embedded in Nanodiscs: How to Manage Non-Specific Interactions in Weak Affinity Chromatography?

Miniaturized weak affinity chromatography is emerging as an interesting alternative to conventional biophysical tools for performing fragment-screening studies in the context of fragment-based drug discovery. In order to push back the analytical limits, it is necessary not only to control non-specific interactions with chromatographic support, but also to adapt this methodology by comparing the results obtained on an affinity column to a control column. The work presented in this study focused on fragment screening that targets a model membrane protein, the adenosine A2A receptor, embedded in nanodiscs (NDs) as biomimetic membranes. By studying the retention behavior of test fragment mixtures on supports modified with different types of NDs, we were able to determine the contribution of ND-related non-specific interactions, in particular the electrostatic effect of anionic phospholipids and the hydrophobic effect of neutral phospholipids. Different strategies for the preparation of control columns (empty NDs, orthosteric site blocking) were investigated and are presented for the first time. With these two types of control columns, the screening enabled the identification of two new fragments of AA2AR, which were confirmed by competition experiments and whose Kd values, estimated directly during the screening or after the competition experiments in frontal mode, were in good agreement.

Effect of dilution solvent and injection volume on the analysis of basic hydrophilic therapeutic polypeptide salts with pressurized carbon dioxide mobile phases.

The chromatographic analysis of long-chain hydrophilic therapeutic peptides, with molecular weight mostly in the 3500-4500 Da range (31-34 amino acids), is explored with pressurized CO2 in the mobile phase. The optimal method was obtained on a Torus 2-PIC column, with a gradient elution of 50-90% co-solvent in CO2, which is relevant of enhanced-fluidity liquid chromatography (EFLC). Both UV (210 nm) and mass spectrometric detection modes were employed to assess the purity of the major peak and its resolution from impurities. Ten out of the eleven peptides in this set were basic, thus they were analyzed as acetate or trifluoroacetate salts. As significant peak distortion was observed in some cases, thorough examination of dilution solvent and injection volume was conducted to improve peak shape and resolution from impurities. Finally, the best injection volume was 1 µL, as any other volume (smaller or larger) yielded distorted peaks, and the best dilution solvent composition was the same as the mobile phase co-solvent (methanol comprising 5% water and 0.1 % methanesulfonic acid). However, not all peptide salts were fully soluble in this solvent so other alternatives (including more water in the dilution solvent), offering adequate dissolution but slightly inferior chromatographic performance should be chosen in such cases.

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.

Chromatographic analysis of biomolecules with pressurized carbon dioxide mobile phases - A review.

Biomolecules like proteins, peptides and nucleic acids widely emerge in pharmaceutical applications, either as synthetic active pharmaceutical ingredients, or from natural products as in traditional Chinese medicine. Liquid-phase chromatographic methods (LC) are widely employed for the analysis and/or purification of such molecules. On another hand, to answer the ever-increasing requests from scientists involved in biomolecules projects, other chromatographic methods emerge as useful complements to LC. In particular, there is a growing interest for chromatography with a mobile phase comprising pressurized carbon dioxide, which can be named either (i) supercritical (or subcritical) fluid chromatography (SFC) when CO2 is the major constituent of the mobile phase, or (ii) enhanced fluidity liquid chromatography (EFLC) when hydro-organic or purely organic solvents are the major constituents of the mobile phase. Despite the low polarity of CO2, supposedly inadequate to solubilize such biomolecules, SFC and EFLC were both employed in many occasions for this purpose. This paper specifically reviews the literature related to the SFC/EFLC analysis of free amino acids, peptides, proteins, nucleobases, nucleosides and nucleotides. The analytical conditions employed for specific molecular families are presented, with a focus on the nature of the stationary phase and the mobile phase composition. We also discuss the potential benefits of combining SFC/EFLC to LC in a single gradient elution, a method sometimes designated as unified chromatography (UC). Finally, detection issues are presented, and more particularly hyphenation to mass spectrometry.

Analysis of short-chain bioactive peptides by unified chromatography-electrospray ionization mass spectrometry. Part I. Method development.

A method to analyse short-chain bioactive peptides (MW < 800 Da) and their impurities was developed with a unified chromatography (UC) analysis, including a wide mobile phase gradient ranging from supercritical fluid to near-liquid conditions, with UV and electrospray ionization mass spectrometry detection (ESI-MS). Four stationary phases and three mobile phase compositions were examined. Ten model peptides were first selected to identify the best operating conditions, including five linear tripeptides and five cyclic pentapeptides, with log P values ranging from -5.9 to 3.6, and including isomeric species. Derringer desirability functions were designed to identify optimal operating conditions based on 7 criteria, namely the number of peaks detected (including all impurities resolved), the proportion of the chromatogram occupied by target peaks, the least favourable resolution observed between the main peptide and impurities, peak shape features (asymmetry and peak width at half height), and finally the signal-to-noise ratio observed both with UV (210 nm) and ESI-MS in positive ionization mode. The optimum conditions were obtained on Ascentis Express OH5 stationary phase, with a mobile phase composed of carbon dioxide and methanol, comprising 2% water and 20 mM ammonium hydroxide. The final gradient program ranged from 5 to 80% co-solvent in CO2, with a reversed flow rate gradient ranging from 3.0 to 1.5 mL/min. Back-pressure was set at 120 bar and the column oven temperature at 60°C. Optimal conditions were applied to a large set of 76 peptides (34 linear tripeptides and 42 cyclic pentapeptides) and provided adequate scattering of the peaks in the retention space, together with some separation of isomeric species, particularly for the cyclic peptides.