Guest Binding Affinities Research Articles

Guest-Induced "Breathing-Helical" Dynamic System of a Porphyrinic Metallo-Organic Cage for Advanced Conformational Manipulation.

Host-guest dynamic systems in coordination-driven metallo-organic cages have gained significant attentions since their promising applications in chiral separation, drug delivery, and catalytical fields. To maximize guest-binding affinity, hosts adopting multiple conformations are widely investigated on their structural flexibility for guest accommodation. In this study, a novel metallo-organic cage S with breathing inner cavity and freely twisted side chains was proposed. Single-crystal X-ray diffraction analyses depicted a characteristic "breathing-helical" dynamic system on the semiflexible framework, which led to an unprecedent co-crystallisation of racemic and symmetric conformations via the encapsulation locking of C70 guests. By taking advantages of the high binding affinity, selective extraction of C70 was realized. This research provides new ideas for the modification on the helicities of metallo-organic cages, which could pave a new way for advanced conformational manipulation of supramolecular host systems.

Mimicking nature’s stereoselectivity through coordination cages

Emulating biology’s recognition properties is challenging yet critical for unlocking innovative solutions in medicine, biotechnology, and materials science. In this issue of Chem, Jonathan R. Nitschke, Dawei Zhang, and co-workers report a series of tetrahedral cages formed by subcomponent self-assembly, which has proven to be highly effective in recognizing complex chiral molecules with exceptional stereoselectivity. Emulating biology’s recognition properties is challenging yet critical for unlocking innovative solutions in medicine, biotechnology, and materials science. In this issue of Chem, Jonathan R. Nitschke, Dawei Zhang, and co-workers report a series of tetrahedral cages formed by subcomponent self-assembly, which has proven to be highly effective in recognizing complex chiral molecules with exceptional stereoselectivity. Enantiopure FeII4L4 cages bind steroids stereoselectivelyLi et al.ChemApril 12, 2023In BriefThe preparation of new enantiopure tetrahedral cages enables the inclusion of steroids with high stereoselectivities. Subtle differences in cavity structure between cage enantiomers lead to major changes in guest binding affinity and even stoichiometry. Our work thus demonstrates how control over host handedness serves as a useful means to gauge and tune the binding of information-rich guests with complex stereochemistries. It also provides insight into how natural stereoselective receptors work and has implications for designing new cage-mediated asymmetric transformations and chemical purification methods. Full-Text PDF Open Access

CASTING: A Potent Supramolecular Strategy to Cytosolically Deliver STING Agonist for Cancer Immunotherapy and SARS-CoV-2 Vaccination

CASTING: A Potent Supramolecular Strategy to Cytosolically Deliver STING Agonist for Cancer Immunotherapy and SARS-CoV-2 Vaccination

Coordination Cages Selectively Transport Molecular Cargoes Across Liquid Membranes.

Chemical purifications are critical processes across many industries, requiring 10–15% of humanity’s global energy budget. Coordination cages are able to catch and release guest molecules based upon their size and shape, providing a new technological basis for achieving chemical separation. Here, we show that aqueous solutions of FeII4L6 and CoII4L4 cages can be used as liquid membranes. Selective transport of complex hydrocarbons across these membranes enabled the separation of target compounds from mixtures under ambient conditions. The kinetics of cage-mediated cargo transport are governed by guest binding affinity. Using sequential transport across two consecutive membranes, target compounds were isolated from a mixture in a size-selective fashion. The selectivities of both cages thus enabled a two-stage separation process to isolate a single compound from a mixture of physicochemically similar molecules.

Enhancement of Alkali Metal Ion Recognition by Metalation of a Tris(saloph) Cryptand Having Benzene Rings at the Bridgeheads.

A cryptand derivative, H6L, which has three H2saloph arms connected by two benzene ring bridgeheads, was synthesized and converted into the trinuclear metallocryptand, LNi3. The nonmetalated host, H6L, was found to bind to alkali metal ions (Na+, K+, Rb+, Cs+; logKa = 3.37-6.67) in its well-defined cavity in DMSO/chloroform (1:9). The binding affinity was enhanced by 1-2 orders of magnitude upon the conversion into the metallocryptand, LNi3, which can be explained by the more polarized phenoxo groups in the [Ni(saloph)] arms. The guest binding affinity of Na+ < K+ < Rb+ ≈ Cs+ was clearly demonstrated by the 1H NMR competition experiments. The DFT calculations suggested that the Rb+ ion most suitably fit into the benzene-benzene spacing with a cation-π interaction and that only the largest Cs+ ion can almost equally interact with all six phenoxo oxygen donor atoms. The metallocryptand, LNi3, also showed a strong binding affinity to Ag+ by taking advantage of cation-π interactions, which was confirmed by spectroscopic titrations and crystallographic analysis as well as DFT calculations. Thus, the well-defined three-dimensional cavity of LNi3 was found to be suitable for strong binding with alkali metal ions as well as Ag+.

Biomimetic Recognition-Based Bioorthogonal Host–Guest Pairs for Cell Targeting and Tissue Imaging in Living Animals

Biomimetic Recognition-Based Bioorthogonal Host–Guest Pairs for Cell Targeting and Tissue Imaging in Living Animals

Synthesis and Guest-Binding Properties of pH/Reduction Dual-Responsive Cyclophane Dimer.

A water-soluble cyclophane dimer having two disulfide groups as a reduction-responsive cleavable bond as well as several acidic and basic functional groups as a pH-responsive ionizable group 1 was successfully synthesized. It was found that 1 showed pH-dependent guest-binding behavior. That is, 1 strongly bound an anionic guest, 6-p-toluidinonaphthalene-2-sulfonate (TNS) with binding constant (K/M−1) for 1:1 host-guest complexes of 9.6 × 104 M−1 at pH 3.8, which was larger than those at pH 7.4 and 10.7 (6.0 × 104 and 2.4 × 104 M−1, respectively), indicating a favorable electrostatic interaction between anionic guest and net cationic 1. What is more, release of the entrapped guest molecules by 1 was easily controlled by pH stimulus. Large favorable enthalpies (ΔH) for formation of host-guest complexes were obtained under the pH conditions employed, suggesting that electrostatic interaction between anionic TNS and 1 was the most important driving force for host-guest complexation. Such contributions of ΔH for formation of host-guest complexes decreased along with increased pH values from acidic to basic solutions. Upon addition of dithiothreitol (DTT) as a reducing reagent to an aqueous PBS buffer (pH 7.4) containing 1 and TNS, the fluorescence intensity originating from the bound guest molecules decreased gradually. A treatment of 1 with DTT gave 2, having less guest-binding affinity by the cleavage of disulfide bonds of 1. Consequently, almost all entrapped guest molecules by 1 were released from the host. Moreover, such reduction-responsive cleavage of 1 and release of bound guest molecules was performed more rapidly in aqueous buffer at pH 10.7.

Precise Assembly and Supramolecular Catalysis of Tetragonal- and Trigonal-Elongated Octahedral Coordination Containers

The construction of distorted or irregular coordination polyhedrons with specific shapes and functionalities is highly challenging. Here, we demonstrate a viable strategy for attaining a severely d...

Crown Ether Functionalized Potassium‐Responsive Anionocages for Cascaded Guest Delivery

AbstractIn many critical biological processes, host–guest chemistry of protein receptors is regulated by effector molecules to realize cascaded delivery of messenger molecules between different targets. Mimicking these natural processes with artificial receptors remains a challenge. Herein, we report a cascaded guest delivery between two anionocages (anion‐coordination‐driven cages), in a reversible manner, wherein binding of K+ ions by a crown ether functionalized, heteroleptic A2L3 (A=anion, L=ligand) anionocage triggers the release and delivery of a TEA+ (tetraethylammonium) guest to another A2L3 anionocage that is a weaker and less K+‐sensitive receptor. Elimination of the K+ with [2,2,2]‐cryptand enables recapture of the TEA+ by the crown ether functionalized anionocage and thus realizes a reversed guest delivery. Moreover, integrative self‐sorting of anionocages is firstly reported, leading to heteroleptic cages with enhanced guest binding affinities.

Crown Ether Functionalized Potassium-Responsive Anionocages for Cascaded Guest Delivery.

In many critical biological processes, host-guest chemistry of protein receptors is regulated by effector molecules to realize cascaded delivery of messenger molecules between different targets. Mimicking these natural processes with artificial receptors remains a challenge. Herein, we report a cascaded guest delivery between two anionocages (anion-coordination-driven cages), in a reversible manner, wherein binding of K+ ions by a crown ether functionalized, heteroleptic A2 L3 (A=anion, L=ligand) anionocage triggers the release and delivery of a TEA+ (tetraethylammonium) guest to another A2 L3 anionocage that is a weaker and less K+ -sensitive receptor. Elimination of the K+ with [2,2,2]-cryptand enables recapture of the TEA+ by the crown ether functionalized anionocage and thus realizes a reversed guest delivery. Moreover, integrative self-sorting of anionocages is firstly reported, leading to heteroleptic cages with enhanced guest binding affinities.

SAMPL7 TrimerTrip host-guest binding affinities from extensive alchemical and end-point free energy calculations.

The prediction of host-guest binding affinities with computational modelling is still a challenging task. In the 7th statistical assessment of the modeling of proteins and ligands (SAMPL) challenge, a new host named TrimerTrip was synthesized and the thermodynamic parameters of 16 structurally diverse guests binding to the host were characterized. In the TrimerTrip-guest challenge, only structures of the host and the guests are provided, which indicates that the predictions of both the binding poses and the binding affinities are under assessment. In this work, starting from the binding poses obtained from our previous enhanced sampling simulations in the configurational space, we perform extensive alchemical and end-point free energy calculations to calculate the host-guest binding affinities retrospectively. The alchemical predictions with two widely accepted charge schemes (i.e. AM1-BCC and RESP) are in good agreement with the experimental reference, while the end-point estimates perform poorly in reproducing the experimental binding affinities. Aside from the absolute value of the binding affinity, the rank of binding free energies is also crucial in drug design. Surprisingly, the end-point MM/PBSA method seems very powerful in reproducing the experimental rank of binding affinities. Although the length of our simulations is long and the intermediate spacing is dense, the convergence behavior is not very good, which may arise from the flexibility of the host molecule. Enhanced sampling techniques in the configurational space may be required to obtain fully converged sampling. Further, as the length of sampling in alchemical free energy calculations already achieves several hundred ns, performing direct simulations of the binding/unbinding event in the physical space could be more useful and insightful. More details about the binding pathway and mechanism could be obtained in this way. The nonequilibrium method could also be a nice choice if one insists to use the alchemical method, as the intermediate sampling is avoided to some extent.

SAMPL6 host-guest binding affinities and binding poses from spherical-coordinates-biased simulations.

Host-guest binding is a challenging problem in computer simulation. The prediction of binding affinities between hosts and guests is an important part of the statistical assessment of the modeling of proteins and ligands (SAMPL) challenges. In this work, the volume-based variant of well-tempered metadynamics is employed to calculate the binding affinities of the host-guest systems in the SAMPL6 challenge. By biasing the spherical coordinates describing the relative position of the host and the guest, the initial-configuration-induced bias vanishes and all possible binding poses are explored. The agreement between the predictions and the experimental results and the observation of new binding poses indicate that the volume-based technique serves as a nice candidate for the calculation of binding free energies and the search of the binding poses.

Rationalizing the Activity of an "Artificial Diels-Alderase": Establishing Efficient and Accurate Protocols for Calculating Supramolecular Catalysis.

Self-assembled cages have emerged as novel platforms to explore bioinspired catalysis. While many different size and shape supramolecular structures are now readily accessible, only a few are known to accelerate chemical reactions under substoichiometric conditions. These limited examples point to a poor understanding of cage catalysis in general, limiting the ability to design new systems. Here we show that a simple and efficient density-functional-theory-based methodology, informed by explicitly solvated molecular dynamics and coupled cluster calculations, is sufficient to accurately reproduce experimental guest binding affinities (MAD = 1.9 kcal mol-1) and identify the catalytic Diels-Alder proficiencies (>80% accuracy) of two homologous Pd2L4 metallocages with a variety of substrates. This analysis reveals how subtle structural differences in the cage framework affect binding and catalysis. These effects manifest in a smaller distortion and more favorable interaction energy for the catalytic cage compared to the inactive structure. This study gives detailed insight that would otherwise be difficult to obtain from experiments, providing new opportunities in the design of catalytically active supramolecular cages.

Exo-Functionalized Metallacages as Host-Guest Systems for the Anticancer Drug Cisplatin.

Within the framework of designing new self-assembled metallosupramolecular architectures for drug delivery, seven [Pd2L4]4+ metallacages (L = 2,6-bis(pyridine-3-ylethynyl)pyridine) featuring different groups in exo-position, selected to enhance the cage solubility in aqueous environment, were synthesized. Thus, carboxylic acids, sugars, and PEG groups were tethered to the bispyridyl ligands directly or via disulfide bond formation, as well as via click chemistry. The ligands and respective cages were characterized by different methods, including NMR spectroscopy and high-resolution electrospray mass spectrometry (HR-ESI-MS). While the two ligands featuring carboxylic acid-functionalized groups showed improved solubility in water, the other ligands were soluble only in organic solvents. Unfortunately, all the respective self-assembled cages were also insoluble in water. Afterwards, the encapsulation properties of the anticancer drug cisplatin in selected [Pd2L4]X4 cages (X = , ) were studied by 1H, 1H DOSY, and 195Pt NMR spectroscopy. The effect of the counter ions as well as of the polarity of the solvent in the drug encapsulation process were also investigated, and provided useful information on the host-guest properties of these experimental drug delivery systems. Our results provide further experimental support for previous studies that suggest the desolvation of guests from surrounding solvent molecules and the resulting solvent rearrangement may actually be the primary driving force for determining guest binding affinities in metallacages, in the absence of specific functional group interactions.

Acid-Regulated Switching of Metal Cation and Anion Guest Binding in Halogen-Bonding Rotaxanes.

The ability of natural enzymes to regulate their guest binding affinities and preferences through the use of co-ligands which alter the features of the binding site is fundamental to biological homeostatic control. Herein, the rarely exploited orthosteric control of guest binding is demonstrated using neutral halogen bonding [2]rotaxanes, in which a chemical stimulus (acid) interacting with the interlocked host binding site switches the host's native guest preference from metal cations to anions. When neutral, the rotaxanes exhibit pronounced transition metal cation affinity and comparatively weak anion binding properties. However, the addition of acid attenuates the rotaxanes' ability to coordinate cations, while concurrently enabling strong binding of halides through charge assisted halogen bonding and hydrogen bonding interactions in competitive aqueous solvent media. The appendage of a fluorescent anthracene reporter group to the rotaxane framework also enables diagnostic sensory responses to cation/anion binding.

A Linear Interaction Energy Model for Cavitand Host–Guest Binding Affinities

Host-guest systems provide excellent models to explore molecular recognition in solution along with relevant technological applications from drug carriers to chemosensors. Here, we present a linear interaction energy (LIE) model to predict the binding affinity in host-guests with remarkable efficiency and predictive power. Using four host families, including cucurbiturils, octa acids, and β-cyclodextrin, and a large set (49) of chemically diverse guests, we demonstrate that binding-affinity predictions with a root mean square error <1.5 kcal/mol from experiments can be obtained with a few nanoseconds of molecular dynamics. The parameters of the LIE model are shown to be transferable among host-guest families, and the quality of the predictionsis essentially force-field independent. Inclusion of the strain energy of the host in the bound state appears to be critically important to improve the quality of the predictions, particularly when the host and the guest have comparable sizes. Unsuccesful predictions for 28 additional highly charged and bulky guests to cucurbit[7]uril indicate future directions for improvement.

Selective cation and anion guest binding in host selenazamacrocycles.

We report selenazamacrocycle hosts that are the first system to change guest binding affinity from cation to anion depending upon macrocycle oxidation/reduction. Selective cation (Fe2+) or anion (BF4-) binding occurs with both ions present and under identical reaction conditions. We also report the first macrocyclic complex with a Fe-Se bond.

Synthesis of a cysteine-linked cyclophane dimer having two rhodamine moieties and its reduction-responsive degradation as studied by fluorescence spectroscopy

Cysteine-linked cyclophane dimer having two rhodamine moieties (2) was synthesized as a reduction-responsive host. Owing to self-quenching property of the two rhodamine moieties, cyclophane dimer 2 showed weak fluorescence intensity relative to that of the rhodamine B moiety itself. The cleavage of disulfide bond of 2 was performed by a treatment with reducing agents such as dithiothreitol, to give the corresponding monomeric cyclophanes having a rhodamine moiety. Such reductive degradation of 2 was detected by the increase on fluorescence intensity. As a host, cyclophane dimer 2 was found to show a stronger guest-binding affinity than the monomeric cyclophanes due to concentration effects of the macrocycles. In addition, reduction-responsive release of entrapped guest molecules by 2 was also monitored by fluorescence spectroscopy.

Synthesis and effect of linker length on guest-binding affinity of water-soluble tetraazacyclophane dimers

Cationic cyclophane dimers which are constructed with two tetraaza[6.1.6.1]para-cyclophanes and a short or long hydrophilic linker interposed between them were synthesized as a water-soluble host (1a and 1b, respectively). The binding constant (K) values of 1a having a short linkage with fluorescence guests such as 6-p-toluidinonaphthalene-2-sulfonate and 6-anilinonaphthalene-2-sulfonate were about 2-fold larger than those of 1b having a long one with the identical guests. Local concentration in the macrocycles of 1a was more effective than that of 1b for such enhancements of the guest-binding affinity. Moreover, the K values of cationic cyclophane dimer having a short hydrophobic linkage 1c were comparable to those by 1a, indicating that guest-binding affinity was less affected on the hydrophilic/hydrophobic characteristics of these short linkers.

Biotinylated Cyclophane: Synthesis, Cyclophane-Avidin Conjugates, and Their Enhanced Guest-Binding Affinity.

Cationic and anionic cyclophanes bearing a biotin moiety were synthesized as a water-soluble host (1a and 1b, respectively). Both hosts 1a and 1b were found to strongly bind avidin with binding constants of 1.3 × 10(8) M(-1), as confirmed by surface plasmon resonance measurements. The present conjugate of 1a with avidin (1a-avidin) showed an enhanced guest binding affinity toward fluorescence guests such as TNS and 2,6-ANS. The K values of 1a-avidin conjugate with TNS and 2,6-ANS were ~19-fold larger than those of monocyclic cyclophane 1a with the identical guests. Favorable hydrophobic and electrostatic interactions between 1a-avidin and TNS were suggested by computer-aided molecular modeling calculations. Moreover, addition of excess biotin to the complexes of 1a-avidin with the guests resulted in dissociation of 1a-avidin to avidin and 1a having less guest-binding affinity. Conversely, such enhancements in the guest-binding affinity were not obviously observed for the conjugate of anionic 1b with avidin (1b-avidin) due to electrostatic repulsion between anionic 1b and anionic guests.