The Influence of Small Biomolecules, Salts and Buffers on the Molecular Recognition of Amide Naphthotube in Aqueous Solutions

We found the binding affinities of amide naphthotube to neutral organic molecules in water are not influenced by most of small biomolecules, inorganic salts, and PBS and Tris buffers but are reduced in HEPES buffer through competitive binding. Nevertheless, salts do change the binding affinities of amide naphthotube to charged molecules through a screening effect.

When Molecules Meet in Water-Recent Contributions of Supramolecular Chemistry to the Understanding of Molecular Recognition Processes in Water

Molecular recognition processes in water differ from those in organic solvents in that they are mediated to a much greater extent by solvent effects. The hydrophobic effect, for example, causes molecules that only weakly interact in organic solvents to stay together in water. Such water-mediated interactions can be very efficient as demonstrated by many of the synthetic receptors discussed in this review, some of which have substrate affinities matching or even surpassing those of natural binders. However, in spite of considerable success in designing such receptors, not all factors determining their binding properties in water are fully understood. Existing concepts still provide plausible explanations why the reorganization of water molecules often causes receptor-substrate interactions in water to be strongly exothermic rather than entropically favored as predicted by the classical view of the hydrophobic effect.

Buffer and Salt Effects in Aqueous Host-Guest Systems: Screening, Competitive Binding, or Both?

There are many open questions regarding the supramolecular properties of ions in water, a fact that has ramifications within any field of study involving buffered solutions. Indeed, as Pielak has noted (Buffers, Especially the Good Kind, Biochemistry, 2021, in press. DOI:10.1021/acs.biochem.1c00200) buffers were conceived of with little regard to their supramolecular properties. But there is a difficulty here; the mathematical models supramolecular chemists use for affinity determinations do not account for screening. As a result, there is uncertainty as to the magnitude of any screening effect and how this compares to competitive salt/buffer binding. Here we use a tetra-cation cavitand to compare halide affinities obtained using a traditional unscreened model and a screened (Debye-Hückel) model. The rule of thumb that emerges is that if ionic strength is changed by >1 order of magnitude─either during a titration or if a comparison is sought between two different buffered solutions─screening should be considered. We also build a competitive mathematical model showing that binding attenuation in buffer is largely due to competitive binding to the host by said buffer. For the system at hand, we find that the effect of competition is approximately twice that of the effect of screening (∼RT at 25 °C). Thus, for strong binders it is less important to account for screening than it is to account for competitive complexation, but for weaker binders both effects should be considered. We anticipate these results will help supramolecular chemists unravel the properties of buffers and so help guide studies of biomacromolecules.

Selective Recognition of Amino Acids and Peptides by Small Supramolecular Receptors

To this day, the recognition and high affinity binding of biomolecules in water by synthetic receptors remains challenging, while the necessity for systems for their sensing, transport and modulation persists. This problematic is prevalent for the recognition of peptides, which not only have key roles in many biochemical pathways, as well as having pharmacological and biotechnological applications, but also frequently serve as models for the study of proteins. Taking inspiration in nature and on the interactions that occur between several receptors and peptide sequences, many researchers have developed and applied a variety of different synthetic receptors, as is the case of macrocyclic compounds, molecular imprinted polymers, organometallic cages, among others, to bind amino acids, small peptides and proteins. In this critical review, we present and discuss selected examples of synthetic receptors for amino acids and peptides, with a greater focus on supramolecular receptors, which show great promise for the selective recognition of these biomolecules in physiological conditions. We decided to focus preferentially on small synthetic receptors (leaving out of this review high molecular weight polymeric systems) for which more detailed and accurate molecular level information regarding the main structural and thermodynamic features of the receptor biomolecule assemblies is available.

Multimode binding and stimuli responsive displacement of acridine orange dye complexed with p-sulfonatocalix[4/6]arene macrocycles

Interaction of acridine orange (AOH+) dye with water soluble anionic p-sulfonatocalix[n]arene (SCXn) hosts, SCX4 and SCX6, having different cavity dimensions, has been investigated using multispectroscopic techniques. Intriguing modulation in the photophysical properties of AOH+ upon interaction with SCXn hosts indicate the formation of different host-guest complexes at different regions of the host concentrations. At lower host concentrations, AOH+ undergoes SCXn assisted aggregation, causing a drastic reduction in fluorescence intensity. At higher host concentrations, aggregated-AOH+-SCXn complexes disintegrate and monomeric-AOH+-SCXn exo and inclusion complexes are eventually formed, leading to a huge fluorescence enhancement finally. Observed effects are more pronounced with SCX6 as compared to SCX4 host. Time-resolved fluorescence studies indicate that at very high host concentrations, there is also a diffusion-controlled dynamic quenching for both monomeric-AOH+-SCXn exo and inclusion complexes, caused by the free SCXn present in the solution, a phenomenon not reported before for such host-guest systems. The aggregated-AOH+-SCXn complexes at lower host concentration were employed to investigate displacement study using an antiviral drug, 1-adamantanamine (AD) and a neurotransmitter, acetylcholine (AcCh), as the competitive binders cum external stimuli, which resulted in a drastic recovery of the fluorescence reduced initially due to aggregation process. Though both the AOH+-SCXn systems act as efficient supramolecular assemblies in sensing AD and AcCh as the analytes through fluorescence "OFF-ON" mechanism, the effect is more pronounced for AOH+-SCX4 system as compared to AOH+-SCX6. SCXn induced interesting modulation in the photophysical properties of AOH+ and the stimulus responsive dye displacement observed for aggregated-AOH+-SCXn systems can expectedly find applications in fluorescence OFF-ON sensing, supramolecular functional materials and similar others.

Counterion effect on sulfonatocalix[n]arene recognition

Sulfonatocalixarenes, like other ionic receptors, possess counterions that can affect the molecular recognition process. In the present review it is shown that the competitive effect of the alkaline cations frequently used as counterions determines not only the magnitude of the external guest association constant, but also the stoichiometry of the complexes. Experimental evidences are shown about the interaction of the counterions with sulfonatocalixarene, allowing to quantify its association equilibrium constants. The counterions recognition will be a competitive process that must be taken into account when investigating the interaction of calixarenes with an external guests. When the external guest is a neutral molecule it will be possible to form ternary complexes where the counterion shows a competitive and cooperative effect. By increasing the size of the receptor, sulfonatocalix[6] and sulfonatocalix[8]arene, the complexity of the system is increased due to the formation of counterion complexes with stoichiometries 1:1 and 1:2. In the presence of an external guest, the formation of heteroternary complexes with 1:1:1 stoichiometries including a counterion and an organic cation will be possible.

A journey from calix[4]arene to calix[6] and calix[8]arene reveals more than a matter of size. Receptor concentration affects the stability and stoichiometric nature of the complexes

An in-depth study provides the basis for an accurate characterization of supramolecular systems based on p-sulfonatocalix[6,8]arenes.

Effect of buffer at nanoscale molecular recognition interfaces – electrostatic binding of biological polyanions

The electrostatic binding of polyanionic heparin by cationic receptors is highly dependent on the buffer in which the binding assay is carried out.