Sequence-defined antibody-recruiting macromolecules.

Antibody-recruiting molecules represent a novel class of therapeutic agents that mediate the recruitment of endogenous antibodies to target cells, leading to their elimination by the immune system. Compared to single-ligand copies, macromolecular scaffolds presenting multiple copies of an antibody-binding ligand offer advantages in terms of increased complex avidity. In this study, we describe the synthesis of sequence-defined macromolecules designed for antibody recruitment, utilising dinitrophenol (DNP) as a model antibody-recruiting motif. The use of discrete macromolecules gives access to varying the spacing between DNP motifs while maintaining the same chain length. This characteristic enables the investigation of structure-dependent binding interactions with anti-DNP antibodies. Through solid-phase thiolactone chemistry, we synthesised a series of oligomers with precisely localised DNP motifs along the backbone and a terminal biotin motif for surface immobilisation. Utilising biolayer interferometry analysis, we observed that oligomers with adjacent DNP motifs exhibited enhanced avidity for anti-DNP antibodies. Molecular modelling provided insights into the structures and dynamics of the various macromolecules, shedding light on the accessibility of the ligands to the antibodies. Overall, our findings highlight that the use of sequence-defined macromolecules can contribute to our understanding of structure-activity relationships and provide insights for the design of novel antibody-recruiting therapeutic agents.

Towards a Rational Design of Antibody-Recruiting Molecules through a Computational Microscopy View of their Interactions with the Target Antibody.

Antibody recruiting molecules (ARMs) are an innovative class of chimeric molecules, consisting of an antibody-binding ligand (ABL) and a target-binding ligand (TBL). ARMs mediate ternary complex formation between a target cell of interest for elimination and endogenous antibodies that are present in human serum. Clustering of fragment crystallizable (Fc) domains on the surface of antibody-bound cells mediate destruction of the target cell by innate immune effector mechanisms. ARMs are typically designed by conjugating small molecule haptens to a (macro)molecular scaffold, without considering the structure of the respective anti-hapten antibody. Here we report on a computational molecular modeling methodology that allows for studying the close contacts between ARMs and the anti-hapten antibody, considering (1) the spacer length between ABL and TBL; (2) the number of ABL and TBL, and (3) the molecular scaffold onto which these are positioned. Our model predicts the difference in binding modes of the ternary complex and predicts which ARMs are optimal recruiters. Avidity measurements of the ARM-antibody complex and ARM-mediated antibody recruitment to cell surfaces in vitro confirmed these computational modeling predictions. This kind of multiscale molecular modelling holds potential for design of drug molecules that rely on antibody binding for their mechanism of action.

Peptoids as a Chiral Stationary Phase for Liquid Chromatography: Insights from Molecular Dynamics Simulations.

Peptoids are peptide regioisomers with attractive structural tunability in terms of sequence and three-dimensional arrangement. Peptoids are foreseen to have a great potential for many diverse applications, including their utilization as a chiral stationary phase in chromatography. To achieve chiral recognition, a chiral side chain is required to allow specific interactions with a given enantiomer from a racemic mixture. One of the most studied chiral stationary phases, built with (S)-N-1-phenylethyl (Nspe) units, was shown to be successful in resolving racemic mixtures of binaphthyl derivatives. However, there is currently no description at the atomic scale of the factors favoring its enantioselectivity. Here, we take advantage of steered molecular dynamics simulations to mimic the elution process at the atomic scale and present evidence that the predominantly right-handed helical conformation of Nspe peptoids and their ability to form stronger hydrogen bonds with the (S) enantiomer are responsible for the chiral recognition of the popular chiral probe 2,2'-bihydroxy-1,1'-binaphthyl.