Retention behaviour of analytes in reversed‐phase high‐performance liquid chromatography—A review

V., Ganesh; Basuri, P. Poorna; Sahini, K.; C.N, Nalini

doi:10.1002/bmc.5482

Cited by 10 publications

(6 citation statements)

References 79 publications

(77 reference statements)

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“…KD scores are widely used for characterizing protein sequences, but they are not reliable predictors of RPLC retention (Figure S2). The reason underlying the limited predictive power of KD scores and related parameters such as logP ,,, is that they only consider the amino acid composition, but not the peptide sequence, structural dynamics, or ion pairing interactions. ,, …”

Section: Resultsmentioning

confidence: 99%

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

Scrosati

Konermann

2023

Anal. Chem.

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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 SiO 2 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.

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Section: Resultsmentioning

confidence: 99%

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

Scrosati

Konermann

2023

Anal. Chem.

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“…For the lipophilicity assessment of the compounds, the octadecyl C18 stationary phase and the less hydrophobic octyl C8 one in the reversed phase (RP) system are the most frequently used [ 4 , 19 , 22 ]. Both columns with such fillings and TLC plates are commercially available and commonly applied.…”

Section: Introductionmentioning

confidence: 99%

Comparison of HPLC, HPTLC, and In Silico Lipophilicity Parameters Determined for 5-Heterocyclic 2-(2,4-Dihydroxyphenyl)-1,3,4-thiadiazoles

Paw,

Śliwa,

Komsta

et al. 2024

Molecules

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The 5-heterocyclic 2-(2,4-dihydroxyphenyl)-1,3,4-thiadiazoles were obtained as potential biologically active compounds. Lipophilicity is one of the most important physicochemical properties of compounds and was already taken into account during the drug candidates design and development. The lipophilicity of compounds was determined using the computational (log P) and chromatography (log kw, RMw) methods. The experimental ones included the reverse-phase column high performance liquid chromatography RP (HPLC) with C8, C18, phosphatidylcholine (IAM), and cholesterol stationary phases and the thin layer chromatography (RP-HPTLC) with C8 and C18 stationary phases and various organic modifiers under the isocratic conditions. Descriptive statistics, correlation, and PCA analyses were used to compare the obtained results. For lipophilicity estimation of the tested compounds by HPTLC, dioxane and MeOH seem to be particularly beneficial as organic modifiers. The chromatographic lipophilicity parameters log kw (RMw) were well correlated and highly redundant (85%) compared with those calculated. Most compounds possess lipophilicity parameters within the recommended range for drug candidates.

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“…At the same experimental conditions, we can get the almost same results on analytes’ retention data. In a chromatographic system, the molecular structure of a compound determines its properties, and further, affect relative affinity for the mobile and stationary phases and, therefore, its retention characteristics ( Roman, 2007 ; Ganesh et al, 2022 ). The quantitative structure-retention relationships (QSRR) have been used as a model approach to establish methods of property prediction ( Roman, 2007 ).…”

Section: Introductionmentioning

confidence: 99%

Development of QSRR model for hydroxamic acids using PCA-GA-BP algorithm incorporated with molecular interaction-based features

Nie

Xia

et al. 2022

Front. Chem.

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As a potent zinc chelator, hydroxamic acid has been applied in the design of inhibitors of zinc metalloenzyme, such as histone deacetylases (HDACs). A series of hydroxamic acids with HDAC inhibitory activities were subjected to the QSRR (Quantitative Structure–Retention Relationships) study. Experimental data in combination with calculated molecular descriptors were used for the development of the QSRR model. Specially, we employed PCA (principal component analysis) to accomplish dimension reduction of descriptors and utilized the principal components of compounds (16 training compounds, 4 validation compounds and 7 test compounds) to execute GA (genetic algorithm)-BP (error backpropagation) algorithm. We performed double cross-validation approach for obtaining a more convincing model. Moreover, we introduced molecular interaction-based features (molecular docking scores) as a new type of molecular descriptor to represent the interactions between analytes and the mobile phase. Our results indicated that the incorporation of molecular interaction-based features significantly improved the accuracy of the QSRR model, (R2 value is 0.842, RMSEP value is 0.440, and MAE value is 0.573). Our study not only developed QSRR model for the prediction of the retention time of hydroxamic acid in HPLC but also proved the feasibility of using molecular interaction-based features as molecular descriptors.

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Retention behaviour of analytes in reversed‐phase high‐performance liquid chromatography—A review

Cited by 10 publications

References 79 publications

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

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

Comparison of HPLC, HPTLC, and In Silico Lipophilicity Parameters Determined for 5-Heterocyclic 2-(2,4-Dihydroxyphenyl)-1,3,4-thiadiazoles

Development of QSRR model for hydroxamic acids using PCA-GA-BP algorithm incorporated with molecular interaction-based features

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