An NMR Method To Pinpoint Supramolecular Ligand Binding to Basic Residues on Proteins

Multivalent Molecular Tweezers Disrupt the Essential NDC80 Interaction with Microtubules

Binding of microtubule filaments by the conserved Ndc80 protein is required for kinetochore-microtubule attachments in cells and the successful distribution of the genetic material during cell division. The reversible inhibition of microtubule binding is an important aspect of the physiological error correction process. Small molecule inhibitors of protein-protein interactions involving Ndc80 are therefore highly desirable, both for mechanistic studies of chromosome segregation and also for their potential therapeutic value. Here, we report on a novel strategy to develop rationally designed inhibitors of the Ndc80 Calponin-homology domain using Supramolecular Chemistry. With a multiple-click approach, lysine-specific molecular tweezers were assembled to form covalently fused dimers to pentamers with a different overall size and preorganization/stiffness. We identified two dimers and a trimer as efficient Ndc80 CH-domain binders and have shown that they disrupt the interaction between Ndc80 and microtubules at low micromolar concentrations without affecting microtubule dynamics. NMR spectroscopy allowed us to identify the biologically important lysine residues 160 and 204 as preferred tweezer interaction sites. Enhanced sampling molecular dynamics simulations provided a rationale for the binding mode of multivalent tweezers and the role of pre-organization and secondary interactions in targeting multiple lysine residues across a protein surface.

Molecular Tweezers: Supramolecular Hosts with Broad-Spectrum Biological Applications

Lysine-selective molecular tweezers (MTs) are supramolecular host molecules displaying a remarkably broad spectrum of biologic activities. MTs act as inhibitors of the self-assembly and toxicity of amyloidogenic proteins using a unique mechanism. They destroy viral membranes and inhibit infection by enveloped viruses, such as HIV-1 and SARS-CoV-2, by mechanisms unrelated to their action on protein self-assembly. They also disrupt biofilm of Gram-positive bacteria. The efficacy and safety of MTs have been demonstrated in vitro, in cell culture, and in vivo, suggesting that these versatile compounds are attractive therapeutic candidates for various diseases, infections, and injuries. A lead compound called CLR01 has been shown to inhibit the aggregation of various amyloidogenic proteins, facilitate their clearance in vivo, prevent infection by multiple viruses, display potent anti-biofilm activity, and have a high safety margin in animal models. The inhibitory effect of CLR01 against amyloidogenic proteins is highly specific to abnormal self-assembly of amyloidogenic proteins with no disruption of normal mammalian biologic processes at the doses needed for inhibition. Therapeutic effects of CLR01 have been demonstrated in animal models of proteinopathies, lysosomal-storage diseases, and spinal-cord injury. Here we review the activity and mechanisms of action of these intriguing compounds and discuss future research directions. SIGNIFICANCE STATEMENT: Molecular tweezers are supramolecular host molecules with broad biological applications, including inhibition of abnormal protein aggregation, facilitation of lysosomal clearance of toxic aggregates, disruption of viral membranes, and interference of biofilm formation by Gram-positive bacteria. This review discusses the molecular and cellular mechanisms of action of the molecular tweezers, including the discovery of distinct mechanisms acting in vitro and in vivo, and the application of these compounds in multiple preclinical disease models.

Protein-Calixarene Complexation: From Recognition to Assembly

ConspectusThis Account summarizes the progress in protein-calixarene complexation, tracing the developments from binary recognition to the glue activity of calixarenes and beyond to macrocycle-mediated frameworks. During the past 10 years, we have been tackling the question of protein-calixarene complexation in several ways, mainly by cocrystallization and X-ray structure determination as well as by solution state methods, NMR spectroscopy, isothermal titration calorimetry (ITC), and light scattering. Much of this work benefitted from collaboration, highlighted here. Our first breakthrough was the cocrystallization of cationic cytochrome c with sulfonato-calix[4]arene leading to a crystal structure defining three binding sites. Together with NMR studies, a dynamic complexation was deduced in which the calixarene explores the protein surface. Other cationic proteins were similarly amenable to cocrystallization with sulfonato-calix[4]arene, confirming calixarene-arginine/lysine encapsulation and consequent protein assembly. Calixarenes bearing anionic substituents such as sulfonate or phosphonate, but not carboxylate, have proven useful.Studies with larger calix[n]arenes (n = 6, 8) demonstrated the bigger better binder phenomenon with increased affinities and more interesting assemblies, including solution-state oligomerization and porous frameworks. While the calix[4]arene cavity accommodates a single cationic side chain, the larger macrocycles adopt different conformations, molding to the protein surface and accommodating several residues (hydrophobic, polar, and/or charged) in small cavities. In addition to accommodating protein features, the calixarene can bind exogenous components such as polyethylene glycol (PEG), metal ions, buffer, and additives. Ternary cocrystallization of cytochrome c, sulfonato-calix[8]arene, and spermine resulted in altered framework fabrication due to calixarene encapsulation of the tetraamine. Besides host-guest chemistry with exogenous components, the calixarene can also self-assemble, with numerous instances of macrocycle dimers.Calixarene complexation enables protein encapsulation, not merely side chain encapsulation. Cocrystal structures of sulfonato-calix[8]arene with cytochrome c or Ralstonia solanacearum lectin (RSL) provide evidence of encapsulation, with multiple calixarenes masking the same protein. NMR studies of cytochrome c and sulfonato-calix[8]arene are also consistent with multisite binding. In the case of RSL, a C₃ symmetric trimer, up to six calixarenes bind the protein yielding a cubic framework mediated by calixarene dimers. Biomolecular calixarene complexation has evolved from molecular recognition to framework construction. This latter development contributes to the challenge in design and preparation of porous molecular materials. Cytochrome c and sulfonato-calix[8]arene form frameworks with >60% solvent in which the degree of porosity depends on the protein:calixarene ratio and the crystallization conditions. Recent developments with RSL led to three frameworks with varying porosity depending on the crystallization conditions, particularly the pH. NMR studies indicate a pH-triggered assembly in which two acidic residues appear to play key roles. The field of supramolecular protein chemistry is growing, and this Account aims to encourage new developments at the interface between biomolecular and synthetic/supramolecular chemistry.

NMR Spectroscopy of supramolecular chemistry on protein surfaces

As one of the few analytical methods that offer atomic resolution, NMR spectroscopy is a valuable tool to study the interaction of proteins with their interaction partners, both biomolecules and synthetic ligands. In recent years, the focus in chemistry has kept expanding from targeting small binding pockets in proteins to recognizing patches on protein surfaces, mostly via supramolecular chemistry, with the goal to modulate protein–protein interactions. Here we present NMR methods that have been applied to characterize these molecular interactions and discuss the challenges of this endeavor.

Progressive Folding and Adaptive Multivalent Recognition of Alkyl Amines and Amino Acids in p-Sulfonatocalix[4]arene Hosts: Solid-State and Solution Studies

Calix[4]arenes have the ability to encapsulate biomimetic guests, offering interesting opportunities to explore their molecular recognition, very close to biological scenarios. In this study, p-sulfonatocalix[4]arene (C4 A) anions and hydrated alkali cations have been used for the in situ recognition of cationic 1,ω-diammonium-alkanes and 1,ω-amino-acids of variable lengths. NMR spectroscopy illustrates that these systems are stable in aqueous solution and the interaction process involves several binding states or stabilized conformations within the C4 A anion, depending of the nature of the guest. DOSY experiments showed that monomeric 1 : 1 host-guest species are present, while the cation does not influence their self-assembly in solution. The folded conformations observed in the solid-state X-ray single-crystal structures shed light on the constitutional adaptivity of flexible chains to environmental factors. Futhermore, a comprehensive screening of 30 single crystal structures helped to understand the in situ conformational fixation and accurate determination of the folded structures of the confined guest molecules, with a compression up to 40 % compared with their linear conformations.

A route to virtually unlimited functionalization of water-soluble p-sulfonatocalix[4]arenes

The functionality of p-sulfonatocalix[4]arenes can be easily extended using the propargylation/CuAAC reaction sequence, which allows the introduction of up to four substituted triazole units to the narrow rims of the macrocycles while maintaining their cone shapes and water solubility and, thus, biomedical applicability.

A giant hybrid organic–inorganic octahedron from a narrow rim carboxylate calixarene

Here we discovered an unprecedented giant octahedral coordination compound bearing 16 Zn²⁺, 12 Na⁺, 8 O²⁻, 4 OH⁻, 13 H₂O and 6 L⁴⁻ ligands [L⁴⁻ = fully deprotonated tetra(carboxymethoxy)calix[4]arene].

Assembly behaviors of calixarene-based amphiphile and supra-amphiphile and the applications in drug delivery and protein recognition

Calixarene is the third generation of supra-molecular compounds after crown ether and cyclodextrin. Amphiphilic calixarene can be obtained by modulation with both hydrophilic group and hydrophobic alkyl chain. Compared with conventional surfactant, amphiphilic calixarene has much lower critical micelle concentration and is much easier to self-assemble into different morphological aggregates. Calixarene-basedsupra-amphiphile can be designed via noncovalent bonds due to the capability of calixarene to recognize surfactant; the binding of a surfactant with calixarene can decrease the critical micelle concentration of surfactant by several times. The calixarene-surfactant complex can self-aggregate to form spherical micelles, vesicles, and spherical nanoparticles, and the aggregation behavior can be controlled by the structures and the molar ratio of surfactant to calixarene and environmental factors. Calixarene-based amphiphile and supra-amphiphile show low cytotoxicity. They can load drugs and assemble into nanocapsules with drugs. The structure of the calixarene-drug complex can respond to external stimuli, rendering the sustained release of the drug and suggesting its potential application as a drug delivery system. Recently, calixarene has also been found to selectively bind proteins, suggesting its prospect in disease diagnosis and intervention treatment in clinics. This review elaborates on the research progress in the self-assembly behaviors of calixarene-based amphiphile and supra-amphiphile and the applications of the calixarenes in drug delivery and protein recognition. The prospectives for the studies are also provided in this review.

Generation of Dynamic Combinatorial Libraries Using Hydrazone-Functionalized Surface Mimetics

Dynamic combinatorial chemistry (DCC) represents an approach, whereby traditional supramolecular scaffolds used for protein surface recognition might be exploited to achieve selective high affinity target recognition. Synthesis, in situ screening and amplification under selection pressure allows the generation of ligands, which bear different moieties capable of making multivalent non‐covalent interactions with target proteins. Generic tetracarboxyphenyl porphyrin scaffolds bearing four hydrazide moieties have been used to form dynamic combinatorial libraries (DCLs) using aniline‐catalyzed reversible hydrazone exchange reactions, in 10 % DMSO, 5 mm NH₄OAc, at pH 6.75. High resolution mass spectrometry (HRMS) was used to monitor library composition and establish conditions under which equilibria were established.

Protein Recognition by Functionalized Sulfonatocalix[4]arenes

The interactions of two mono-functionalized sulfonatocalix[4]arenes with cytochrome c were investigated by structural and thermodynamic methods. The replacement of a single sulfonate with either a bromo or a phenyl substituent resulted in altered recognition of cytochrome c as evidenced by X-ray crystallography. The bromo-substituted ligand yielded a new binding mode in which a self-encapsulated calixarene dimer contributed to crystal packing. This ligand also formed a weak halogen bond with the protein. The phenyl-substituted ligand was bound to Lys4 of cytochrome c, in a 1.7 Å resolution crystal structure. A dimeric packing arrangement mediated by ligand-ligand contacts in the crystal suggested a possible assembly mechanism. The different protein recognition properties of these calixarenes are discussed.