Bifunctional backbone modified squaramide dipeptides as amyloid beta (Aß) aggregation inhibitors.

Alzheimer's disease (AD) is a devastating neurodegenerative condition with complex pathophysiology. Aggregated amyloid beta (Aß) peptide plaques and higher concentrations of bio-metals such as copper (Cu), zinc (Zn), and iron (Fe) are the most significant hallmarks of AD observed in the brains of AD patients. Therefore simultaneous inhibition of Aß peptide aggregation and reduction of metal stress may serve as an effective therapeutic approach for treating Alzheimer's disease. A series of bifunctional dipeptides bearing squaramide backbone were synthesized and investigated for their ability to chelate metal ions and prevent Aß peptide aggregation. Dipeptides with Valine (V) and Threonine (T) substitutions at the C-terminus exhibited preferential chelation with Cu(II), Zn(II), and Fe(III) metal ions in the presence of other metal ions. They were also found to inhibit the aggregation of Aß peptide in-vitro. A further molecular dynamics (MD) simulation study demonstrated that these two dipeptides interact with the Aß peptide in the hydrophobic core (KLVFF) region. Circular dichroism (CD) study revealed slight conformational change in the Aß peptide upon the interactions with dipeptides. Apart from metal chelation and inhibition of Aß peptide aggregation, the selected dipeptides were found to possess anti-oxidant properties. Therefore, the squaramide backbone-modified dipeptides may serve as an active bifunctional scaffold towards the development of new chemical entities for the treatment of Alzheimer's disease.

Expanding the squaramide library as mycobacterial ATP synthase inhibitors: Innovative synthetic pathway and biological evaluation.

Mycobacterial ATP synthase is a validated therapeutic target for combating drug-resistant tuberculosis. Inhibition of this enzyme has been featured as an efficient strategy for the development of new antimycobacterial agents against drug-resistant pathogens. In this study, we synthesised and explored two distinct series of squaric acid analogues designed to inhibit mycobacterial ATP synthase. Among the extensive array of compounds investigated, members of the phenyl-substituted sub-library emerged as primary hits. To gain deeper insights into their mechanisms of action, we conducted advanced biological studies, focusing on the compounds displaying a direct binding of a nitrogen heteroatom to the phenyl ring, resulting in the highest potency. Our investigations into spontaneous mutants led to the validation of a single point mutation within the atpB gene (Rv1304), responsible for encoding the ATP synthase subunit a. This genetic alteration sheds light on the molecular basis of resistance to squaramides. Furthermore, we explored the possibility of synergy between squaramides and the reference drug clofazimine using a checkerboard assay, highlighting the promising avenue for enhancing the effectiveness of existing treatments through combined therapeutic approaches. This study contributes to the expansion of investigating squaramides as promising drug candidates in the ongoing battle against drug-resistant tuberculosis.

Interaction of Ions in Organic and Aqueous Media with an Ion-Pair Sensor Equipped with a BODIPY Reporter: An ON1-OFF-ON2-ON3 Fluorescent Assay.

Here, we present a ditopic ion-pair sensor, B1, containing the BODIPY reporter unit in its structure, which is shown to be able-thanks to the presence of two heterogeneous binding domains-to interact with anions in an enhanced manner in the presence of cations. This enables it to interact with salts even in 99% aqueous solutions, making B1 a good candidate in terms of visual salt detection in the aquatic environment. Receptor B1's ability to extract and release salt was applied in the transport of potassium chloride through a bulk liquid membrane. Working with a concentration of B1 in the organic phase and with the presence of a specific salt in an aqueous solution, an inverted transport experiment was also demonstrated. By varying the type and the amount of the anions added to B1, we were able to develop diverse optical responses, including a unique four-step ON1-OFF-ON2-ON3 output.

Divergent Asymmetric Total Synthesis of (-)-Voacafricines A and B.

A divergent asymmetric total synthesis of voacafricines A and B, hexacyclic monoterpene indole alkaloids, has been accomplished featuring the following key steps: a) a catalyst-controlled asymmetric Pictet-Spengler reaction of 6-methoxytryptamine with a chiral α-ketoester affording a 1,1-disubstituted tetrahydro-ß-carboline in excellent yield and diastereoselectivity; b) oxidative cleavage of a 3,5-disubstituted cyclopentene furnishing a dialdehyde intermediate, which was effectively differentiated through spontaneous cyclization with the neighboring hydroxy and secondary amine functions; c) intramolecular nucleophilic addition of a tertiary amino nitrogen atom to the in situ generated oxonium species generating stereoselectively an unprecedented 8-alkyl octahydro-2H-5,8-methanofuro[2,3-b]azepin-8-ium motif bearing five contiguous stereocenters. The synthesis confirmed the absolute configuration of these two natural products.

Chemically Fueled Communication Along a Scaffolded Nanoscale Array of Squaramides.

Relaying conformational change over several nanometers is central to the function of allosterically regulated proteins. Replicating this mechanism artificially would provide important communication tools, but requires nanometer-sized molecules that reversibly switch between defined shapes in response to signaling molecules. In this work, 1.8 nm long rigid rod oligo(phenylene-ethynylene)s are scaffolds for switchable multi-squaramide hydrogen-bond relays. Each relay can adopt either a parallel or an antiparallel orientation relative to the scaffold; the preferred orientation is dictated by a director group at one end. An amine director responded to proton signals, with acid-base cycles producing multiple reversible changes in relay orientation that were reported by a terminal NH, which is 1.8 nm distant. Moreover, a chemical fuel acted as a dissipative signal. As the fuel was consumed, the relay reverted to its original orientation, illustrating how information from out-of-equilibrium molecular signals can be communicated to a distant site.

Enantioselective synthesis of coumarins catalyzed by an isosteviol-derived tertiary amine-squaramide catalyst.

A newly tertiary amine-squaramide organocatalyst has been successfully developed and applied into the asymmetric Michael addition of 4-hydroxycoumarin to ß,γ-unsaturated α-ketoesters. The catalyst system performed well with a low catalyst loading of 1 mol% under mild reaction conditions. A series of coumarin derivatives were obtained in good to high yields (up to 97%) with high enantioselectivities (up to 96% ee).

Squaramide-Tethered Sulfonamides and Coumarins: Synthesis, Inhibition of Tumor-Associated CAs IX and XII and Docking Simulations.

(1) Background: carbonic anhydrases (CAs) are attractive targets for the development of new anticancer therapies; in particular, CAs IX and XII isoforms are overexpressed in numerous tumors. (2) Methods: following the tail approach, we have appended a hydrophobic aromatic tail to a pharmacophore responsible for the CA inhibition (aryl sulfonamide, coumarin). As a linker, we have used squaramides, featured with strong hydrogen bond acceptor and donor capacities. (3) Results: Starting from easily accessible dimethyl squarate, the title compounds were successfully obtained as crystalline solids, avoiding the use of chromatographic purifications. Interesting and valuable SARs could be obtained upon modification of the length of the hydrocarbon chain, position of the sulfonamido moiety, distance of the aryl sulfonamide scaffold to the squaramide, stereoelectronic effects on the aromatic ring, as well as the number and type of substituents on C-3 and C-4 positions of the coumarin. (4) Conclusions: For sulfonamides, the best profile was achieved for the m-substituted derivative 11 (Ki = 29.4, 9.15 nM, CA IX and XII, respectively), with improved selectivity compared to acetazolamide, a standard drug. Coumarin derivatives afforded an outstanding selectivity (Ki > 10,000 nM for CA I, II); the lead compound (16c) was a strong CA IX and XII inhibitor (Ki = 19.2, 7.23 nM, respectively). Docking simulations revealed the key ligand-enzyme interactions.

Thermoreversible Polymorph Transitions in Supramolecular Polymers of Hydrogen-Bonded Squaramides.

Hydrogen-bonded squaramide (SQ) supramolecular polymers exhibit uncommon thermoreversible polymorph transitions between particle- and fiber-like nanostructures. SQs 1-3, with different steric bulk, self-assemble in solution into particles (AggI) upon cooling to 298 K, and SQs 1 and 2, with only one dendronic group, show a reversible transformation into fibers (AggII) by further decreasing the temperature to 288 K. Nano-DSC and UV/Vis studies on SQ 1 reveal a concentration-dependent transition temperature and ΔH for the AggI-to-AggII conversion, while the kinetic studies on SQ 2 indicate the on-pathway nature of the polymorph transition. Spectroscopic and theoretical studies reveal that these transitions are triggered by the molecular reorganization of the SQ units changing from slipped to head-to-tail hydrogen bonding patterns. This work unveils the thermodynamic and kinetic aspects of reversible polymorph transitions that are of interest to develop stimuli-responsive systems.

Influence of the Z/E Isomerism on the Pathway Complexity of a Squaramide-Based Macrocycle.

The rising interest on pathway complexity in supramolecular polymerization has prompted the finding of novel monomer designs able to stabilize kinetically trapped species and generate supramolecular polymorphs. In the present work, the exploitation of the Z/E (geometrical) isomerism of squaramide (SQ) units to produce various self-assembled isoforms and complex supramolecular polymerization pathways in methylcyclohexane/CHCl3 mixtures is reported for the first time. This is achieved by using a new bissquaramidic macrocycle (MSq) that self-assembles into two markedly different thermodynamic aggregates, AggA (discrete cyclic structures) and AggB (fibrillar structures), depending on the solvent composition and concentration. Remarkably, UV-vis, 1 H NMR, and FT-IR experiments together with quantum-chemical calculations indicate that these two distinct aggregates are formed via two different hydrogen bonding patterns (side-to-side in AggA and head-to-tail in AggB) due to different conformations in the SQ units (Z,E in AggA and Z,Z in AggB). The ability of MSq to supramolecularly polymerize into two distinct aggregates is utilized to induce the kinetic-to-thermodynamic transformation from AggA to AggB, which occurs via an on-pathway mechanism. It is believed that this system provides new insights for the design of potential supramolecular polymorphic materials by using squaramide units.

Fluorescence Recognition of Anions Using a Heteroditopic Receptor: Homogenous and Two-Phase Sensing.

In contrast to monotopic receptor 3, the anthracene functionalized squaramide dual-host receptor 1 is capable of selectively extracting sulfate salts, as was evidenced unambiguously by DOSY, mass spectrometry, fluorescent and ion chromatography measurements. The receptors were investigated in terms of anion and ion pair binding using the UV-vis and 1H NMR titrations method in acetonitrile. The reference anion receptor 3, lacking a crown ether unit, was found to lose the enhancement in anion binding induced by the presence of cations. Besides the ability to bind anions in an enhanced manner exhibited by ion pair receptors 2 and 4, changing the 1-aminoanthracene substituent resulted in their exhibiting a lower anion affinity than receptor 1. By using receptor 1 and adjusting the water content in organic phase it was possible to selectively detect sulfates both by "turn-off" and "turn-on" fluorescence, and to do so homogenously and under interfacial conditions. Such properties of receptor 1 have allowed the development of a new type of sensor capable of recognizing and extracting potassium sulfate from the aqueous medium across a phase boundary, resulting in an appropriate fluorescent response in the organic solution.

Switching-On Fluorescence by Copper (II) and Basic Anions: A Case Study with a Pyrene-Functionalized Squaramide.

The new symmetric acyclic N,N'-bis(1-pyrenyl) squaramide (H2L) functionalized with the pyrene moiety as a fluorogenic fragment has been designed and its ability to selectively detect specific anions and metals investigated. H2L selectively binds Cl- both in solution (DMSO 0.5% H2O and MeCN) and in the solid state, and allows to selectively detect Cu2+ in MeCN with the formation of a 2:1 metal-receptor complex, with a green intense emission appreciable by naked eye under the UV lamp. The H2L copper complex preserves its emission properties in the presence of Cl-. The addition of basic anions (OH-, CN-, and F-) up to 10 equivalents caused the deprotonation of the squaramide NHs and a dramatic change of the emission properties of the H2L copper complex.

Chiral Aminoalcohols and Squaric Acid Amides as Ligands for Asymmetric Borane Reduction of Ketones: Insight to In Situ Formed Catalytic System by DOSY and Multinuclear NMR Experiments.

A series of squaric acid amides (synthesized in 66-99% isolated yields) and a set of chiral aminoalcohols were comparatively studied as ligands in a model reaction of reduction of α-chloroacetophenone with BH3•SMe2. In all cases, the aminoalcohols demonstrated better efficiency (up to 94% ee), while only poor asymmetric induction was achieved with the corresponding squaramides. A mechanistic insight on the in situ formation and stability at room temperature of intermediates generated from ligands and borane as possible precursors of the oxazaborolidine-based catalytic system has been obtained by 1H DOSY and multinuclear 1D and 2D (1H, 10/11B, 13C, 15N) NMR spectroscopy of equimolar mixtures of borane and selected ligands. These results contribute to better understanding the complexity of the processes occurring in the reaction mixture prior to the possible oxazaborolidine formation, which play a crucial role on the degree of enantioselectivity achieved in the borane reduction of α-chloroacetophenone.

Unraveling the Origin of Differentiable 'Turn-On' Fluorescence Sensing of Zn2+ and Cd2+ Ions with Squaramides.

A squaramide ring conjugated with Schiff-bases decorated with hydroxy and methoxy functional groups differentially senses zinc and cadmium ions, which turn on the fluorescence. The feebly emitting free ligands light up in the presence of zinc and cadmium acetates, with the acetate ion playing a pivotal role as a conjugate anion. The selective and differentiable emission responses for zinc and cadmium ions make these ligands efficient multi-analyte sensing agents. Furthermore, these ligands could be used to differentially sense zinc and cadmium ions even in aqueous environments. The NMR investigations reveal marginal differences in the binding of zinc and cadmium ions to the ligands, whereas density functional theory calculations suggest the different extent of ligand-to-metal charge transfer (LMCT) contributes to the differential behavior. Finally, comparison of the excited-state dynamics of free ligand and the metal complexes reveal the appearance of longer lifetime (about 500-700 ps) component with complexation, due to rigidified molecular skeleton, thereby impeding the non-radiative processes.

Synthesis and biological evaluation of new long-chain squaramides as anti-chagasic agents in the BALB/c mouse model.

Chagas Disease is caused by infection with the insect-transmitted protozoan Trypanosoma cruzi and affects more than 10 million people. It is a paradigmatic example of a chronic disease without an effective treatment in Latin America where the current therapies, based on Benznidazole and Nifurtimox, are characterised by limited efficacy, toxic side-effects and frequent failures in the treatment. We present a series of new long-chain squaramides, identified based on their 1H and 13C NMR spectra, and their trypanocidal activity and cytotoxicity were tested in vitro through the determination of IC50 values. Compounds 4 and 7 were more active and less toxic than the reference drug Benznidazole, and these results were the basis of promoting in vivo assays, where parasitaemia levels, assignment of cure, reactivation of parasitaemia and others parameters were determined in mice treated in both the acute and chronic phases. Finally, the mechanisms of action were elucidated at metabolic and mitochondrial levels and superoxide dismutase inhibition. The experiments allowed us to select compound 7 as a promising candidate for treating Chagas Disease, where the activity, stability and low cost make long-chain squaramides appropriate molecules for the development of an affordable anti-chagasic agent versus current treatments.

Bifunctional Squaramide Organocatalysts for the Asymmetric Addition of Formaldehyde tert-Butylhydrazone to Simple Aldehydes.

The nucleophilic addition of formaldehyde tert-butylhydrazone to simple aldehydes (a formal hetero-carbonyl-ene reaction) can be performed with good reactivity and excellent enantioselectivity by virtue of the dual hydrogen-bonding activation exerted by amide-squaramide organocatalysts. The resulting hydroxydiazenes (azo alcohols) were isolated in high yields as enantiomerically enriched azoxy compounds after a regioselective azo-to-azoxy transformation. Subsequent derivatization provides an entry to relevant amino alcohols, oxazolidinones, and derivatives thereof.

The Role of N-Methyl Squaramides in a Hydrogen-Bonding Strategy to Fold Peptidomimetic Compounds.

Small peptides and peptomimetic compounds are valuable tools to probe and study biological systems. Small synthetic peptide analogues adopt a given secondary structure driven by structural modules that organize the compound architecture. Among them, ß- and α-turn mimetics are widely used. This work reports SQ4 and SQ5 squaramido-based turn modules that combine tertiary and secondary squaramide bonds in their structure to control their conformational properties. The efficacy of this combination has been evaluated to promote folding in peptide-like compounds to obtain parallel and antiparallel-hairpin model compounds in hydrogen-bonding competitive media. Crystallographic structures of model compounds and conformational studies based on NMR spectroscopic analysis of the squaramido-peptides confirm that secondary-tertiary squaramides are more prone to adopt the E,Z-conformation than di-secondary squaramides, and consequently are more suitable to gain conformational control over foldable peptidomimetic compounds.

Supramolecular Hydrogels Based on Minimalist Amphiphilic Squaramide-Squaramates for Controlled Release of Zwitterionic Biomolecules.

Supramolecular hydrogels with tunable properties have innovative applications in biomedicine, catalysis, and materials chemistry. Minimalist low-molecular-weight hydrogelators based on squaramide and squaramic acid motifs have been designed. This approach benefits from the high acidity of squaramic acids and the aromaticity of squaramides. Moreover, substituents on the aryl ring tune the π density of the arylsquaramide motif. Thus, materials featuring distinct thermal and mechanical properties have been successfully prepared. The hydrogel (G'≈400 Pa, G''≈57 Pa; at 1.0 % w/v; 1 Hz) obtained from 4-nitrophenylsquaramide motif 1 is thermoreversible (T=57 °C at 0.2 % w/v), thixotropic, self-healable, and undergoes irreversible shrinking in response to saline stress. Furthermore, the hydrogel is injectable and can be loaded with substantial amounts (5:1 excess molar ratio) of zwitterionic biomolecules, such as l-carnitine, γ-aminobutyric acid (GABA), or d,l-Ala-d,l-Ala, without any loss of structural integrity. Then, the release of these molecules can be modulated by saline solutions.

Squaramide-Catalyzed Asymmetric Reactions.

Bifunctional squaramides have emerged as powerful hydrogen-bonding catalysts for promoting a wide array of useful asymmetric reactions, which provides convenient methods for the construction of complex molecular structures and chiral biologically active compounds. This review highlights the recent advances of our research group in the chiral squaramide-catalyzed asymmetric reactions, including Michael addition, Mannich reaction, aza-Henry reaction, Strecker reaction as well as cascade or sequential reactions.

Applications of Chiral Squaramides: From Asymmetric Organocatalysis to Biologically Active Compounds.

This review seeks to provide coverage on the recent advances in chiral squaramide-catalyzed asymmetric transformations and their applications in the synthesis of a variety of chiral biologically active compounds. It aims to give an overview highlighting the new reaction types and enantioenriched medicinal scaffolds developed in the last few years.

Effective anti-leishmanial activity of minimalist squaramide-based compounds.

In order to evaluate the in vitro leishmanicidal activity of N,N'-Squaramides derivatives, compounds that feature both hydrogen bond donor and acceptor groups and are capable of multiple interactions with complementary sites, against Leishmania infantum, Leishmania braziliensis and Leishmania donovani a series of 18compounds was prepared and assayed on extracellular and intracellular parasite forms. Infectivity and cytotoxicity tests were performed on J774.2 macrophage cells using meglumine antimoniate (Glucantime) as the reference drug. Changes in metabolite excretion by 1H-NMR and the ultrastructural alterations occurring in the parasites treated using transmission electron microscopy (TEM), was analyzed. Compounds 1, 7, 11, 14 and 17 were the more active and less toxic. Infection rates showed that the order of effectiveness was 17 > 11 > 14 > 7 for both L. infantum and L. braziliensis and in the same way, the compound 1 for L. donovani. All these compounds have altered the typical structure of the promastigotes, glycosomes and mitochondria. These severe modifications by the compounds are the ultimate reasons for the alterations observed in the excretion products. The Squaramide 17 (3-(butylamino)-4-((3-(dimetilamino)propyl)(methyl)amino)cyclobut-3-en-1,2-dione) was clearly the most efficient of all compounds. The data appear to confirm that the severe modifications generated in organelles such as glycosomes or mitochondria by the compounds are the ultimate reasons for the alterations observed in the excretion products of all species. The activity, stability, low cost of starting materials, and straightforward synthesis make amino squaramides appropriate molecules for the development of an affordable anti-leishmanial agent.