Molecular modeling to rationalize ligand–support interactions in affinity chromatography

Abstract

The development of rational design criteria for synthetic-ligand-based affinity chromatography requires a basic comprehension of all the factors influencing the binding capacity and selectivity of the stationary phase. In this work, molecular dynamics simulations are systematically used to investigate the impact of structural modifications of spacer and ligand on ligand-support interactions. The investigated ligands are characterized by a triazine core bi-functionalized with two amino acid side chains aimed at representing a range of hydrophobic/hydrophilic characters. As spacers both literature (1-2-diaminoethane and 1,4-substituted [1,2,3]-triazole) and speculative oligopeptidic molecules (Gly-[Ala]4-Gly, Gly-[Lys]4-Gly, and Gly-[Glu]4-Gly) have been considered to address the role of charges distribution, rigidity, and structural complexity. In this investigation, the spacer emerged as a key component: on the one hand, the choice of a proper spacer allows improving the hydrophilic character of the ligand-spacer adduct without compromising the structure of the affinity ligand, while on the other hand the use of structurally complex spacers induces spacer-support interactions that enhance the degree of solvation of the ligand regardless of its hydrophobic character. These findings suggest that the use of structured spacers could represent a viable pathway for tailoring the performances of affinity chromatography stationary phases.

An Experimental Framework for Developing Point-of-Need Biosensors: Connecting Bio-Layer Interferometry and Electrochemical Impedance Spectroscopy

“…In addition to these experimental techniques, in silico simulation of ligand-analyte relationships are powerful for informing experimental work, and vice versa . Use of computer simulations for studying biomolecule interplay has been reviewed extensively [ 36 , 37 , 38 , 39 , 40 ].…”

Affibody-Binding Ligands

“…Similarly, all variable amino-acid positions on the peptide ligands were denoted as "active" while the GSG (Gly-Ser-Gly) spacer was defined as not being involved in the interaction to account for the directionality of binding. To simulate the orientation that the peptide assumes when conjugated onto a chromatographic support, in fact, the GSG trimer was constrained to be non-interacting to any of the target affibodies [71]. Docking proceeded through a three-stage protocol: (1) rigid, (2) semi-flexible, and (3) water-refined fully flexible docking.…”

Targeted purification development enabled by computational biophysical modeling

“…In most applications of QSAR or QSPR, detailed analyses are limited to the affinity ligands due to the complexity and computational cost of performing detailed atomistic modeling of these complex interactions. Hence, only a subset of the key features important for protein–ligand interaction as it pertains to purification is captured by the use of such computational modeling to direct bioprocess development . The challenge in the application of such an approach is to discern key but subtle differences in ligands and proteins that influence biologics purification pertaining to affinity and selectivity.…”

“…Hence, only a subset of the key features important for protein-ligand interaction as it pertains to purification is captured by the use of such computational modeling to direct bioprocess development. 18 The challenge in the application of such an approach is to discern key but subtle differences in ligands and proteins that influence biologics purification pertaining to affinity and selectivity. A limitation of this approach to directed process development is that the effect of specific mutations on chromatographic separation can go undetected.…”