Complexes of carboxylato pillar[6]arene with Brooker-type merocyanines: Spectral properties, pKa shifts and the design of a displacement assay for trimethyl lysine

Fluorometric detection and analog discrimination of melatonin by amide naphthotube-based indicator displacement assays

Melatonin, a hormone synthesized by the pineal gland, is renowned for its pivotal role in governing circadian rhythms and its promising therapeutic attributes encompassing anti-inflammatory, anti-aging, and cancer-preventative properties. Nevertheless, the improper utilization of melatonin may lead to health hazards, highlighting the critical necessity for accurate detection of melatonin in pharmaceutical or biological samples. Furthermore, melatonin metabolites exhibit analogous chemical structures yet divergent pathophysiological functions, emphasizing the significance of distinguishing between these analogs. In this study, we report a supramolecular sensor that combines amide naphthotube and toluidine blue O in an indicator displacement assay for the quantitative detection of melatonin and differentiation of its analogs. The sensor demonstrated remarkable sensitivity, with a low detection limit of approximately 0.70 μM, and a broad dynamic range of 0.70-98.8 μM, along with excellent selectivity and stability. Notably, the sensor enables the determination of melatonin levels in various sample matrices, including milk, artificial urine, and pharmaceutical preparations. Through optimization of the host-guest complex ratio, our newly designed sensor effectively distinguishes melatonin from its six analogs. This approach addresses a current research gap, as existing macrocycles have limited capability to differentiate between melatonin analogs, with only a few achieving precise melatonin quantification.

Methodological and force field effects in the molecular dynamics-based prediction of binding free energies of host-guest systems

As a contribution to the understanding and rationalization of methodological and modeling effects in recent host-guest SAMPL challenges, using an alchemical molecular dynamics technique we have examined the impact of force field parameterization and ionic strength in connection with guest charge neutralization on computed dissociation free energies in two typical SAMPL heavily charged macrocyclic hosts encapsulating small protonated amines with disparate binding affinities. We have shown that the methodological treatment for host neutralization, with explicit ions or with the background neutralizing plasma in the context of alchemical calculations under periodic boundary conditions, has a moderate effect on the calculated affinities. On the other hand, we have shown that seemingly small differences in the force field parameterization in highly symmetric hosts can produce systematic effects on the structural features that can have a significant impact on the predicted binding affinities.

SAMPL9 blind predictions using nonequilibrium alchemical approaches

We present our blind predictions for the Statistical Assessment of the Modeling of Proteins and Ligands (SAMPL), ninth challenge, focusing on the binding of WP6 (carboxy-pillar[6]arene) with ammonium/diammonium cationic guests. Host-guest binding free energies have been calculated using the recently developed virtual double system single box approach, based on the enhanced sampling of the bound and unbound end-states followed by fast switching nonequilibrium alchemical simulations [M. Macchiagodena et al., J. Chem. Theory Comput. 16, 7160 (2020)]. As far as Pearson and Kendall coefficients are concerned, performances were acceptable and, in general, better than those we submitted for calixarenes, cucurbituril-like open cavitand, and beta-cyclodextrines in previous SAMPL host-guest challenges, confirming the reliability of nonequilibrium approaches for absolute binding free energy calculations. In comparison with previous submissions, we found a rather large mean signed error that we attribute to the way the finite charge correction was addressed through the assumption of a neutralizing background plasma.

Binding Methylarginines and Methyllysines as Free Amino Acids: A Comparative Study of Multiple Host Classes*

Methylated free amino acids are an important class of targets for host‐guest chemistry that have recognition properties distinct from those of methylated peptides and proteins. We present comparative binding studies for three different host classes that are each studied with multiple methylated arginines and lysines to determine fundamental structure‐function relationships. The hosts studied are all anionic and include three calixarenes, two acyclic cucurbiturils, and two other cleft‐like hosts, a clip and a tweezer. We determined the binding association constants for a panel of methylated amino acids using indicator displacement assays. The acyclic cucurbiturils display stronger binding to the methylated amino acids, and some unique patterns of selectivity. The two other cleft‐like hosts follow two different trends, shallow host (clip) following similar trends to the calixarenes, and the other more closed host (tweezer) binding certain less‐methylated amino acids stronger than their methylated counterparts. Molecular modelling sheds some light on the different preferences of the various hosts. The results identify hosts with new selectivities and with affinities in a range that could be useful for biomedical applications. The overall selectivity patterns are explained by a common framework that considers the geometry, depth of binding pockets, and functional group participation across all host classes.