Macrocyclic receptors for anion recognition

Macrocyclic receptors have emerged as versatile and efficient molecular tools for the recognition and sensing of anions, playing a pivotal role in molecular recognition and supramolecular chemistry. The following review provides an overview of the recent advances in the design, synthesis, and applications of macrocyclic receptors specifically tailored for anion recognition. The unique structural features of macrocycles, such as their well-defined structures and pre-organised binding sites, contribute to their exceptional anion-binding capabilities that have led to their application across a broad range of the chemical and biological sciences.

Reaction contest: hydrolysis versus intramolecular cyclisation reaction in alkyl squaramate esters

The stability and hydrolytic behavior of squaramate esters in aqueous solutions have been investigated. The structure of squaramates and the nature of adjacent groups significantly influence their aqueous stability and reactivity towards nucleophiles. Squaramate esters, lacking or containing weakly basic neighboring group participation (NGP) substitutions, remain stable up to pH 9. Their hydrolysis rate (k OH ≈ 10-1 M-1 s-1) is 1000 times faster than that of squaramides, following a second-order rate law. Squaramate esters functionalized with basic NGP groups, such as amines, display a pH-dependent hydrolysis rate due to anchimeric assistance of the terminal amino group, reducing stability to pH 5. However, when the squaramate ester has a terminal nucleophilic group in the γ position of the alkyl chain, it undergoes rapid intramolecular cyclization, forming cyclic squaramides.

Squaramide-based receptors in anion supramolecular chemistry: insights into anion binding, sensing, transport and extraction

Over the last 15 years, squaramide-based receptors have attracted the attention of supramolecular chemists working in the field of anion recognition. Herein, we highlight examples of squaramide-based receptors that are able to bind, sense, extract and transport anions.

Anion-Binding Properties of Aliphatic Symmetric Squaramide Receptors

Squaramides (SQs), which are very popular for their H-bonding ability, have attracted great interest due to their wide range of applications such as asymmetric synthesis, pharmacology, and anion transportation. In this study, aliphatic symmetric SQs based on cis/trans-1,2-diaminocyclohexane (DACH) substituted with cyclic tertiary amines, synthesized in four steps under simple reaction conditions, were investigated for the first time for their ability to bind Cl-, Br-, and I- anions. The changes in cis/trans geometric isomers and the cyclic ring (pyrrolidine vs piperidine) were found to have a combined effect on the degree of anion binding. The spectroscopic titrations of the SQs with TBA-Cl, TBA-Br, and TBA-I in the range of 0.2 to 20.0 equiv were monitored by 1H NMR, and the analyses of the magnitude of chemical shift differences in the NH peaks of the SQs in course of titration were performed by DynaFit and BindFit programs for the calculation of their Ka values. All symmetric SQs I-IV were found to selectively bind Cl- anion more strongly than Br- anion to varying degrees depending on the SQ derivatives. Especially, SQ IV, which has a symmetric trans-DACH and a pyrrolidine ring, was found to have the highest Cl- anion-binding ability compared to the other SQs. However, the SQs did not show any change in the chemical shift of the NH proton in 1H NMR upon successive addition of TBA-I, indicating that they do not interact with I- anion. The stoichiometries of the complexation behavior of SQs I-IV toward Cl- and Br- anions were also analyzed by Job plots.

Oxocarbon Acids and their Derivatives in Biological and Medicinal Chemistry

The biological and medicinal chemistry of the oxocarbon acids 2,3- dihydroxycycloprop-2-en-1-one (deltic acid), 3,4-dihydroxycyclobut-3-ene-1,2-dione (squaric acid), 4,5-dihydroxy-4-cyclopentene-1,2,3-trione (croconic acid), 5,6-dihydroxycyclohex- 5-ene-1,2,3,4-tetrone (rhodizonic acid) and their derivatives is reviewed and their key chemical properties and reactions are discussed. Applications of these compounds as potential bioisosteres in biological and medicinal chemistry are examined. Reviewed areas include cell imaging, bioconjugation reactions, antiviral, antibacterial, anticancer, enzyme inhibition, and receptor pharmacology.

Squaramides enhance NLRP3 inflammasome activation by lowering intracellular potassium

The NLRP3 inflammasome is a component of the inflammatory response to infection and injury, orchestrating the maturation and release of the pro-inflammatory cytokines interleukin-1β (IL-1β), IL-18, and triggering pyroptotic cell death. Appropriate levels of NLRP3 activation are needed to avoid excessive tissue damage while ensuring host protection. Here we report a role for symmetrical diarylsquaramides as selective K+ efflux-dependent NLRP3 inflammasome enhancers. Treatment of macrophages with squaramides potentiated IL-1β secretion and ASC speck formation in response to K+ efflux-dependent NLRP3 inflammasome activators without affecting priming, endosome cargo trafficking, or activation of other inflammasomes. The squaramides lowered intracellular K+ concentration which enabled cells to respond to a below-threshold dose of the inflammasome activator nigericin. Taken together these data further highlight the role of ion flux in inflammasome activation and squaramides as an interesting platform for therapeutic development in conditions where enhanced NLRP3 activity could be beneficial.

Fatty Acid-Activated Proton Transport by Bisaryl Anion Transporters Depolarises Mitochondria and Reduces the Viability of MDA-MB-231 Breast Cancer Cells

In respiring mitochondria, the proton gradient across the inner mitochondrial membrane is used to drive ATP production. Mitochondrial uncouplers, which are typically weak acid protonophores, can disrupt this process to induce mitochondrial dysfunction and apoptosis in cancer cells. We have shown that bisaryl urea-based anion transporters can also mediate mitochondrial uncoupling through a novel fatty acid-activated proton transport mechanism, where the bisaryl urea promotes the transbilayer movement of deprotonated fatty acids and proton transport. In this paper, we investigated the impact of replacing the urea group with squaramide, amide and diurea anion binding motifs. Bisaryl squaramides were found to depolarise mitochondria and reduce MDA-MB-231 breast cancer cell viability to similar extents as their urea counterpart. Bisaryl amides and diureas were less active and required higher concentrations to produce these effects. For all scaffolds, the substitution of the bisaryl rings with lipophilic electron-withdrawing groups was required for activity. An investigation of the proton transport mechanism in vesicles showed that active compounds participate in fatty acid-activated proton transport, except for a squaramide analogue, which was sufficiently acidic to act as a classical protonophore and transport protons in the absence of free fatty acids.

Protonophoric and mitochondrial uncoupling activity of aryl-carbamate substituted fatty acids

Aryl-urea substituted fatty acids are protonophores and mitochondrial uncouplers that utilise a urea-based synthetic anion transport moiety to carry out the protonophoric cycle. Herein we show that replacement of the urea group with carbamate, a functional group not previously reported to possess anion transport activity, produces analogues that retain the activity of their urea counterparts. Thus, the aryl-carbamate substituted fatty acids uncouple oxidative phosphorylation and inhibit ATP production by collapsing the mitochondrial proton gradient. Proton transport proceeds via self-assembly of the deprotonated aryl-carbamates into membrane permeable dimeric species, formed by intermolecular binding of the carboxylate group to the carbamate moiety. These results highlight the anion transport capacity of the carbamate functional group.

Transmembrane Transport of Bicarbonate by Anion Receptors

The development of synthetic anion transporters is motivated by their potential application as treatment for diseases that originate from deficient anion transport by natural proteins. Transport of bicarbonate is important for crucial biological functions such as respiration and digestion. Despite this biological relevance, bicarbonate transport has not been as widely studied as chloride transport. Herein we present an overview of the synthetic receptors that have been studied as bicarbonate transporters, together with the different assays used to perform transport studies in large unilamellar vesicles. We highlight the most active transporters and comment on the nature of the functional groups present in active and inactive compounds. We also address recent mechanistic studies that have revealed different processes that can lead to net transport of bicarbonate, as well as studies reported in cells and tissues, and comment on the key challenges for the further development of bicarbonate transporters.

Calix[6]arenes with halogen bond donor groups as selective and efficient anion transporters

Here we present the anion binding and anion transport properties of a series of calix[6]arenes decorated on their small rim with either halogen bond or hydrogen bond donating groups. We show that the halogen bond donating iodotriazole groups enable highly selective transport of chloride and nitrate anions, without transport of protons or hydroxide, at rates similar to those observed with thiourea or squaramide groups.

A calix[6]arene with three preorganised halogen bond donating groups gives >100-fold selectivity for Cl⁻ uniport over HCl symport, in contrast to analogous compounds with strong hydrogen bond donating groups.

A Simulation Model for the Non-Electrogenic Uniport Carrier-Assisted Transport of Ions across Lipid Membranes

Impressive work has been completed in recent decades on the transmembrane anion transport capability of small synthetic transporters from many different structural classes. However, very few predicting models have been proposed for the fast screening of compound libraries before spending time and resources on the laboratory bench for their synthesis. In this work, a new approach is presented which aims at describing the transport process by taking all the steps into explicit consideration, and includes all possible experiment-derived parameters. The algorithm is able to simulate the macroscopic experiments performed with lipid vesicles to assess the ion-transport ability of the synthetic transporters following a non-electrogenic uniport mechanism. While keeping calculation time affordable, the final goal is the curve-fitting of real experimental data—so, to obtain both an analysis and a predictive tool. The role and the relative weight of the different parameters is discussed and the agreement with the literature is shown by using the simulations of a virtual benchmark case. The fitting of real experimental curves is also shown for two transporters of different structural type.

Mechanistic Understanding from Molecular Dynamics in Pharmaceutical Research 2: Lipid Membrane in Drug Design

We review the use of molecular dynamics (MD) simulation as a drug design tool in the context of the role that the lipid membrane can play in drug action, i.e., the interaction between candidate drug molecules and lipid membranes. In the standard "lock and key" paradigm, only the interaction between the drug and a specific active site of a specific protein is considered; the environment in which the drug acts is, from a biophysical perspective, far more complex than this. The possible mechanisms though which a drug can be designed to tinker with physiological processes are significantly broader than merely fitting to a single active site of a single protein. In this paper, we focus on the role of the lipid membrane, arguably the most important element outside the proteins themselves, as a case study. We discuss work that has been carried out, using MD simulation, concerning the transfection of drugs through membranes that act as biological barriers in the path of the drugs, the behavior of drug molecules within membranes, how their collective behavior can affect the structure and properties of the membrane and, finally, the role lipid membranes, to which the vast majority of drug target proteins are associated, can play in mediating the interaction between drug and target protein. This review paper is the second in a two-part series covering MD simulation as a tool in pharmaceutical research; both are designed as pedagogical review papers aimed at both pharmaceutical scientists interested in exploring how the tool of MD simulation can be applied to their research and computational scientists interested in exploring the possibility of a pharmaceutical context for their research.

Hydrazones in anion transporters: the detrimental effect of a second binding site

Synthetic anion transporters can be developed using anion receptors that are able to bind the anion and stabilize it in the lipophilic interior of a bilayer membrane, and they usually contain functional groups with acidic NHs, such as ureas, thioureas and squaramides. To assess the suitability of acylhydrazones as a new functional group for the preparation of anion transporters, we have studied a family of thioureas functionalized with these and related functional groups. ¹H NMR titrations and DFT calculations indicate that the thioureas bearing acylhydrazone groups behave as chloride receptors with two separate binding sites, of which the acylhydrazone binds weaker than the thiourea. Chloride transport studies show that the additional binding site has a detrimental effect on thiourea-based transporters, and this phenomenon is also observed for bis(thio)ureas with two separate binding sites. We propose that the presence of a second anion binding unit hinders the transport activity of the thiourea due to additional interactions with the phospholipids of the membrane. In agreement with this hypothesis, extensive molecular dynamics simulations suggest that the molecules will tend to be positioned in the water/lipid interface, driven by the interaction of the NHs of the thiourea and of the acylhydrazone groups with the POPC polar head groups and water molecules. Moreover, the interaction energies show that the poorest transporters have indeed the strongest interactions with the membrane phospholipids, inhibiting chloride transport. This detrimental effect of additional functional groups on transport activity should be considered when designing new ion transporters, unless these groups cooperatively promote anion recognition and transmembrane transport.

Supramolecular chemistry in lipid bilayer membranes

Lipid bilayer membranes form compartments requisite for life. Interfacing supramolecular systems, including receptors, catalysts, signal transducers and ion transporters, enables the function of the membrane to be controlled in artificial and living cellular compartments. In this perspective, we take stock of the current state of the art of this rapidly expanding field, and discuss prospects for the future in both fundamental science and applications in biology and medicine.

Transmembrane anion transport promoted by thioamides

Thioamide groups represent useful hydrogen-bonding motifs for the development of active transmembrane anion transporters. Using a 1,8-di(thioamido)carbazole scaffold the superior performance of thioamides compared with the parent amides has been demonstrated.

Redox-controlled chalcogen and pnictogen bonding: the case of a sulfonium/stibonium dication as a preanionophore for chloride anion transport

Our interest in the chemistry of tunable chalcogen and pnictogen bond donors as Lewis acidic platforms for the complexation and transport of anions has led us to investigate examples of such compounds that can be activated by redox events. Here, we describe the synthesis of [o-MePhS(C6H4)SbPh3]2+ ([3]2+) and [o-MePhS(C6H4)Sb(p-Tol)3]2+ ([4]2+), two dicationic stibonium/sulfonium bifunctional Lewis acids which were obtained by methylation of the phenylthioether derivatives [o-PhS(C6H4)SbPh3]+ ([1]+) and [o-PhS(C6H4)Sb(p-Tol)3]+ ([2]+), respectively. An evaluation of the chloride anion transport properties of these derivatives using chloride-loaded POPC unilamellar vesicles shows that the activity of the monocations [1]+ and [2]+ greatly exceeds that of the dications [3]2+ and [4]2+, a phenomenon that we assign to the higher lipophilicity of the monocationic compounds. Harnessing this large transport activity differential, we show that [4]2+ can be used as a prechloridophore that is readily activated by reduction of the sulfonium moiety. Indeed, [4]2+ reacts with GSH to afford [2]+ as an active transporter. This activation, which has been monitored in aqueous solution, can also be carried out in situ, in the presence of the chloride-loaded POPC unilamellar vesicles.

Advances in anion transport and supramolecular medicinal chemistry

Advances in anion transport by synthetic supramolecular systems are discussed in this article. Developments in the design of discrete molecular carriers for anions and supramolecular anion channels are reviewed followed by an overview of the use of these systems in biological systems as putative treatments for diseases such as cystic fibrosis and cancer.

Simple squaramide receptors for highly efficient anion binding in aqueous media and transmembrane transport

A family of acyclic squaramide receptors (L1–L5) have been synthesised with the aim to evaluate how the presence of additional H-bond donor groups on the squaramide scaffold could affect their affinity towards anions and transport ability.

Squaramide-based synthetic chloride transporters activate TFEB but block autophagic flux

Cystic fibrosis is a disease caused by defective function of a chloride channel coupled to a blockade of autophagic flux. It has been proposed to use synthetic chloride transporters as pharmacological agents to compensate insufficient chloride fluxes. Here, we report that such chloride anionophores block autophagic flux in spite of the fact that they activate the pro-autophagic transcription factor EB (TFEB) coupled to the inhibition of the autophagy-suppressive mTORC1 kinase activity. Two synthetic chloride transporters (SQ1 and SQ2) caused a partially TFEB-dependent relocation of the autophagic marker LC3 to the Golgi apparatus. Inhibition of TFEB activation using a calcium chelator or calcineurin inhibitors reduced the formation of LC3 puncta in cells, yet did not affect the cytotoxic action of SQ1 and SQ2 that could be observed after prolonged incubation. In conclusion, the squaramide-based synthetic chloride transporters studied in this work (which can also dissipate pH gradients) are probably not appropriate for the treatment of cystic fibrosis yet might be used for other indications such as cancer.

Fluorinated synthetic anion carriers: experimental and computational insights into transmembrane chloride transport

A series of fluorinated tripodal tris-thioureas function as highly active anion transporters across lipid bilayers and cell membranes. Here, we investigate their mechanism of action using anion transport assays in cells and synthetic vesicles and molecular modelling of transporter-lipid interactions. When compared with non-fluorinated analogues, fluorinated compounds demonstrate a different mechanism of membrane transport because the free transporter cannot effectively diffuse through the membrane. As a result, in H+/Cl- cotransport assays, fluorinated transporters require the presence of oleic acid to form anionic oleate complexes for recycling of the transporter, whereas non-fluorinated analogues readily diffuse through the membrane as free transporters and show synergistic transport with the proton transporter gramicidin. Molecular dynamics simulations revealed markedly stronger transporter-lipid interactions for fluorinated compounds compared with non-fluorinated analogues and hence, higher energy barriers for fluorinated compounds to cross the membrane as free transporters. With use of appropriate proton transporters to ensure measurement of the correct rate-limiting steps, the transport rates determined in synthetic vesicle assays show excellent agreement with the anion transport rates determined in cell-based assays. We conclude that integration of computational and experimental methods provides a strategy to optimise transmembrane anion transporter design for biomedical applications.

Fluorescent squaramide ligands for cellular imaging and their encapsulation in cubosomes

Two new fluorescent squaramides bearing quinoline (L1) and naphthalene (L2) as fluorogenic fragments were synthesized and investigated as possible cellular imaging probes as free molecules and when loaded in monoolein-based cubosomes.