Noncovalent Research Articles

His-tag based supramolecular biopolymerization.

The term supramolecular polymer has been applied to polymeric materials in which the individual units, i.e., building blocks-are bound to each other via noncovalent interactions, including electrostatic or hydrogen bonding, as well as metal-ligand conjugation. The building blocks are generally low molecular weight amphiphiles. Methods for preparing biopolymers based on non-toxic, metal-ligand conjugation have been little studied; however, they offer significant potential for tuning the response of biologically relevant macromolecules. In this communication, we characterize the assembly and morphology of supramolecular biopolymers in which the building blocks are low- or medium-molecular weight globular proteins-ubiquitin and Cas9-interacting via metal-ligand conjugation. In each case, the protein gene was expressed in cell culture with the addition of hexa-His/linkers at both the N and C termini. Divalent cations investigated were Zn2+ and Ni2+. We observe in cryo-TEM imaging an absolute requirement for divalent cations for the formation of supramolecular biopolymers. In the presence of Ni2+, 1D assembled fibers are predominant, while with Zn2+, the more frequently detected structures are sheet-like. We use gel electrophoresis and CD spectroscopy to monitor possible secondary and tertiary structural changes in the protein building blocks during conjugation.

The Feasibility of Using Electrostatic Interactions for Immobilizing Ru-bda Catalysts in Covalent Organic Framework: A Proof-of-Concept.

Heterogenization of molecular catalysts effectively resolves the separation issues of homogeneous catalysts and expands their application scenarios. In recent years, more and more studies have been using non-covalent interactions to achieve the heterogenization of molecular catalysts. Herein, electrostatic attraction was used to immobilize molecular catalysts, Ru-bda small molecular catalysts in COF materials, where the charged Ru-bda catalysts were immobilized in the oppositely charged COF with a high [Ru] loading content of ~0.2 mmol [Ru] g-1 COF. The leakage experiment verified that the immobilization of Ru-bda catalysts in COF by electrostatic interactions is stable in 0.1 M HClO4 and less than 5 % of molecular Ru-bda catalysts were leached into the solution in 2 hours. The chemical water oxidation experiment was conducted as a model catalysis reaction to verify the feasibility of using electrostatic interactions for immobilizing Ru-bda catalysts in COFs. The prepared Ru(bda)@COFs demonstrate a high catalytic activity of 268 μmol L-1 s-1 O2 for chemical water oxidation, illustrating the electrostatic attractions between COF and small molecules that can be used to immobilize homogeneous catalysts in heterogeneous materials. However, the robustness of COF material itself under catalytic conditions should be considered in practical applications.

Utilizing MEDT analysis of [3 + 2] cycloaddition reaction: x-ray crystallography of spirooxindole linked with thiophene/furan heterocycles and triazole framework.

Hybridization of spirooxindole with different pharmacophores such as triazole and heterocycle such as thiophene and furan moiety was achieved by the [3 + 2] cycloaddition (32CA) reaction approach. Structural investigations of the compounds 4a and 4b were performed using X-ray single crystal structure determinations and Hirshfeld analysis. Both compounds crystallized in monoclinic crystal system. The space group is P21/c for 4a and P21/n for 4b. The crystal parameters are a = 10.2619(3) Å, b = 13.6776(3) Å, c = 10.9318(3), β = 116.640(4)° for the former while a = 13.0012(1) Å, b = 14.9692(1) Å, c = 14.1178(1) Å, β = 97.101(1)° for the latter. In both compounds, the aryl group and the triazole moieties are twisted from one another. The twist angle is 84.75˚for 4a while 86.64˚ for 4b. Based on Hirshfeld calculations, the Cl…H, O…H, N…H and C…H non-covalent interactions in 4a while the O…H interactions in 4b are the most important. The molecular mechanism of the key 32CA reaction between the in situ generated azomethine ylides and the corresponding chalcones has been studied within the Molecular Electron Density Theory (MEDT). The MEDT study reveals that the low activation energies and high experimental selectivity are the result of the supernucleophilic character of the ylides and the strong electrophilicity of the chalcones, which favour the process through a high polar character. This high polar character accounts for the total endo selectivity experimentally found.

Protein-based 2D Nanoarchitectures Constructed by Heterochiral π-Stacking Dimerization of Helical Foldamers.

In this study, we focus on the designability and controllability of the interaction interface between secondary structures, and discover an important interface interaction between helical secondary structures by non-covalent synthesis along the helical axis. The formation of discrete heterochiral dimers consisting of left-handed helix and right-handed helix not only helps to discover nonclassical supramolecular chirality phenomena, but also enables controllable protein assembly. Highly ordered nanostructures were thus constructed using p-stacking dimerization of helical foldamers to control tetrameric avidin proteins. The designable and modifiable primitives of artificial folded molecules enable the modification of secondary structure interfaces through non-covalent interactions, leading to the generation of unique structures and functions. These findings are of fundamental importance to the understanding of the precise assembly process of helical foldamers and can provide insights to facilitate the rational design of abiotic protein-like tertiary structures and further functionalization.

Evolution Enhances Kemp Eliminase Activity by Optimizing Oxyanion Stabilization and Conformational Flexibility.

The base-promoted Kemp elimination reaction has been used as a model system for enzyme design. Among the multiple computationally designed and evolved Kemp eliminases generated along the years, the HG3-to-HG3.17 evolutionary trajectory is particularly interesting due to the high catalytic efficiency of HG3.17 and the debated role of glutamine 50 (Gln50) as potential oxyanion stabilizer. This study aims to elucidate the structural and dynamic changes along the evolutionary pathway from HG3 to HG3.17 that contribute to improved catalytic efficiency. In particular, we evaluate key variants along the HG3 evolutionary trajectory via molecular dynamics simulations coupled to non-covalent interactions and water analysis. Our computational study indicates that HG3.17 can adopt a catalytically competent conformation promoted by a water-mediated network of non-covalent interactions, in which aspartate 124 is properly positioned for proton abstraction and both glutamine 50 and mutation cysteine 84 contribute to oxyanion stabilization. We find that HG3.17 exhibits a rather high flexibility of Gln50, which is regulated by the conformation adopted by the active site residue Trp44. This interplay between Gln50 and Trp44 positioning induced by distal active site mutations affects the water-mediated network of non-covalent interactions, Gln50 preorganization, and water content of the active site pocket.

Abstract PR007: To the tumor and beyond: Tales of a holistic miRNA delivery vehicle

Abstract Like the challenges and skepticism that faced the antibody therapeutics field over a decade ago, RNA therapeutics is facing the same. And, like the antibody therapeutics field, we are beginning to realize the clinical impact of RNA therapeutics amiss these challenges. This is most clearly highlighted with the recent approval of mRNA vaccines and RNAi drugs targeted to the liver. Unfortunately, RNA-based drugs targeted to tumors is lagging behind, even with countless years of work that has revealed the power of using RNAi for treating oncological diseases. Lack of success is attributed to inability to deliver RNAi safely and effectively. A successful delivery agent requires multiple features. First, the agent must deliver the RNA specifically to the intended cells. Second, the agent must have a large therapeutic window, meaning that toxicity, if observed, should occur at doses that are orders of magnitude higher than the therapeutic dose. Third, if delivery of the RNA is by way of a specific ligand and receptor pair, as is the case herein, the RNA must successfully escape the endosome. Simply swelling the endosome is not enough if noncovalent interactions between the ligand and the receptor cannot be disrupted. Fourth, the RNA should include appropriate stabilizing modifications to increase intracellular half-life that will reduce dosing and cost. Through hard work and dedication, we have come up with an inclusive, easily synthesized, intramolecular molecule that achieves all of these essential features. Here, the challenges we face, the hurdles we have overcome, and the barriers that still remain with achieving success in reveling the clinical potential of miRNAs as anti-cancer therapeutics will be presented. Citation Format: Andrea L Kasinski. To the tumor and beyond: Tales of a holistic miRNA delivery vehicle [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: RNAs as Drivers, Targets, and Therapeutics in Cancer; 2024 Nov 14-17; Bellevue, Washington. Philadelphia (PA): AACR; Mol Cancer Ther 2024;23(11_Suppl):Abstract nr PR007.

The E3 ligase HUWE1 interacts with ubiquitin non-covalently via key residues in the HECT domain.

HUWE1, a HECT E3 ligase, is critical for processes like protein degradation and tumor development. Contrary to previous findings which suggested minimal non-covalent interactions between the HUWE1 HECT domain and ubiquitin, we identified a non-covalent interaction between the HUWE1 HECT N-lobe and ubiquitin using NMR spectroscopy, revealing a conserved ubiquitin-binding mode shared across HECT E3 ligases. Molecular dynamics simulations not only confirmed the stability of this interaction but also uncovered conformational changes in key residues, which likely influence binding affinity. Additionally, we highlighted the roles of both conserved and unique residues in ubiquitin binding. These findings advance our understanding of the interactions between the HUWE1 HECT domain and ubiquitin, and highlight potential targets for therapeutic intervention in the ubiquitin-proteasome pathway.

Fine-Tuning Porous Structure of Zirconium-Based Metal-Organic Frameworks for Efficient Separation and Purification of Astaxanthin by Defect Engineering.

Efficient separation of bioactive compounds from nature source, particularly that of astaxanthin (AXT), remains challenging due to their low content in complicated matrix and readily degradable structure. Herein, a modulator-induced defect engineering is presented on the stable zirconium-based metal-organic frameworks (Zr-MOFs) to optimize pore size and pore chemistry for the efficient separation and purification of AXT for the first time. High adsorption capacity of 26.21mgg-1 is achieved on the best-performing defect Zr-MOF (d-UiO-67-4), superior over the other reported adsorbent for AXT. Meanwhile, d-UiO-67-4 exhibits the selective adsorption of AXT over other carotenoids analogues with similar structure and properties. This is attributed to the preferential non-covalent interactions between defect framework and AXT revealed by the spectroscopy analysis and density functional theory (DFT) calculations. High purity of AXT with 89.0%±2.3% extraction efficiency can be realized after the purification of AXT by d-UiO-67-4. The practical separation performance of d-UiO-67-4 for AXT extracted from Haematococcus pluvialis is demonstrated by fixed-bed column-based dynamic adsorption and desorption experiments. This work broadens the preparation methods for thermosensitive active substances and provided new research ideas for the controlled adsorption of functional food factors.

Harnessing Cross-strand π-π Interlocking for Synergistic Enhancement of Immune Checkpoint Blocking and Ferroptosis.

The dynamic nature of noncovalent bonds in peptide self-assembly allows for selective accommodation of guest molecules. However, it remains unclear how to harness coassembly to reinforce the host peptides and simultaneously improve the application defects of guest molecules. This study aims to achieve supramolecular synergy between the host and guest, further expanding the functional space of the hybrid nanostructures. Herein, we utilized the aromatic regions present in β-sheet peptides to accommodate aromatic molecules, forming long-range nanotubes (NQ40@AIF) through a unique 'cross-strand π-π interlocking'. This strategy not only stabilizes the coassembly effectively but also synergizes the biological functions of the host and guest molecules. Moreover, due to the chemical diversity of the coassembled NQ40@AIF, it exhibits advantages in tumor combination therapy, achieving effective synergy between ferroptosis and immune checkpoint blocking. This work provides a minimalistic strategy for constructing peptide nanostructures with complex functionalities.

Skeletal Editing of Energetic Materials: Acid-Catalyzed One-Step Synthesis of Bridged Triazoles as High-Energy-Density Materials via the Nef Reaction.

Thermally stable insensitive energetic materials have captivated significant attention from the global research community due to their potential impact. In this study, a series of symmetric and asymmetric nitromethyl-bridged triazole compounds were synthesized from pyrimidine moieties via a skeletal editing approach. Additionally, carbonyl-bridged compounds were synthesized in a single step by using acid-catalyzed Nef reactions from their nitromethyl precursors. Peripheral modifications of pyrimidine resulted in fused energetic moieties. All synthesized compounds were fully characterized by using infrared spectroscopy, high-resolution mass spectrometry, multinuclear magnetic resonance spectroscopy, elemental analysis, and differential scanning calorimetry. Single-crystal X-ray diffraction analysis confirmed the structures of compounds 4 and 10. The newly synthesized moieties exhibit densities ranging from 1.75 to 1.86 g cm-3, detonation velocities between 8044 and 8608 m s-1, and detonation pressures between 23.10 and 30.31 GPa. Notably, compounds 9 and 10 demonstrate exceptional heat resistance, with decomposition temperatures of 315 and 335 °C, respectively. Computational studies, including density functional theory, quantum theory of atoms in molecules, noncovalent interactions, and electrostatic surface potential analysis, account for hydrogen-bonding and noncovalent interactions. This work highlights the potential of skeletal editing in the development of high-performing, thermally stable energetic materials.

Lone Pair-π Interactions in Organic Reactions.

Noncovalent interactions between a lone pair of electrons and π systems can be categorized into two types based on the nature of π systems. Lone pair-π(C═O) interactions with π systems of unsaturated, polarized bonds are primarily attributed to orbital interactions, whereas lone pair-π(Ar) interactions with π systems of aromatic functional groups result from electrostatic attractions (for electron-deficient aryls) or dispersion attractions and Pauli repulsions (for electron-rich/neutral aryls). Unlike well-established noncovalent interactions, lone pair-π interactions have been comparatively underappreciated or less used to influence reaction outcomes. This review emphasizes experimental and computational studies aimed at integrating lone pair-π interactions into the design of catalytic systems and utilizing these interactions to regulate the reactivity and selectivity of chemical transformations. The role of lone pair-π interactions is highlighted in the stabilization or destabilization of transition states and ground-state binding. Examples influenced by lone pair-π interactions with both unsaturated, polarized bonds and aromatic rings as π systems are included. At variance with previous reviews, the present review is not structured according to the physical origin of particular classes of lone pair-π interactions but is divided into chapters according to ways in which lone pair-π interactions affect kinetics and/or selectivity of reactions.

Graph Neural Networks with Multi-features for Predicting Cocrystals using APIs and Coformers Interactions.

Active pharmaceutical ingredients (APIs) have gained direct pharmaceutical interest, along with their in vitro properties, and thus utilized as auxiliary solid dosage forms upon FDA guidance and approval on pharmaceutical cocrystals when reacting with coformers, as a potential and attractive route for drug substance development. However, screening and selecting suitable and appropriate coformers that may potentially react with APIs to successfully form cocrystals is a time-consuming, inefficient, economically expensive, and labour-intensive task. In this study, we implemented GNNs to predict the formation of cocrystals using our introduced API-coformers relational graph data. We further compared our work with previous studies that implemented descriptor-based models (e.g., random forest, support vector machine, extreme gradient boosting, and artificial neural networks). All built graph-based models show compelling performance accuracies (i.e., 91.36, 94.60 and 95. 95% for GCN, GraphSAGE, and RGCN respectively). RGCN demonstrated effectiveness and prevailed among the built graph-based models due to its capability to capture intricate and learn nuanced relationships between entities such as non-ionic and non-covalent interactions or link information between APIs and coformers which are crucial for accurate predictions and representations. These capabilities allows the model to adeptly learn the topological structure inherent in the graph data.

Polyurethanes Made with Blends of Polycarbonates with Different Molecular Weights Showing Adequate Mechanical and Adhesion Properties and Fast Self-Healing at Room Temperature

Dynamic non-covalent interactions between polycarbonate soft segments have been proposed for explaining the intrinsic self-healing of polyurethanes synthesized with polycarbonate polyols (PUs) at 20 °C. However, these self-healing PUs showed insufficient mechanical properties, and their adhesion properties have not been explored yet. Different PUs with self-healing at 20 °C, acceptable mechanical properties, and high shear strengths (similar to the highest ones reported in the literature) were synthesized by using blends of polycarbonate polyols of molecular weights 1000 and 2000 Da (CD1000 + CD2000). Their structural, thermal, rheological, mechanical, and adhesion (single lap-shear tests) properties were assessed. PUs with higher CD1000 polyol contents exhibited shorter self-healing times and dominant viscous properties due to the higher amount of free carbonate groups, significant carbonate–carbonate interactions, and low micro-phase separation. As the CD2000 polyol content in the PUs increased, slower kinetics and longer self-healing times and higher mechanical and adhesion properties were obtained due to a dominant rheological elastic behavior, soft segments with higher crystallinities, and greater micro-phase separation. All PUs synthesized with CD1000 + CD2000 blends exhibited a mixed phase due to interactions between polycarbonate soft segments of different lengths which favored the self-healing and mobility of the polymer chains, resulting in increased mechanical properties.

Cryostructuring of Polymeric Systems: 68. Evaluation of Poly(vinyl alcohol) Composite Cryogels Filled with Poly(3-hydroxybutyric acid)-Based Microspheres of Different Porous Morphology as Potential Delivery Systems for Drugs of Various Water-Solubility

Poly(3-hydroxybutyric acid)-based microspheres of two types, with and without macropores, were prepared; their morphology and particle size were evaluated. These microspheres were entrapped as disperse fillers into the bulk of macroporous cryogels based on poly(vinyl alcohol) (PVA). It was found that the rigidity of the resultant composite cryogels increased markedly as compared to that of unfilled cryogels of the same PVA concentration. The resulting composites were further tested for their potential to act as drug carriers. With that, simvastatin was included into the filler particles directly in the course of their preparation, followed by entrapment of such drug-loaded microspheres into the PVA cryogel. In turn, ibuprofen sodium salt was introduced into the preliminary prepared cryogels filled with the drug-free microspheres. The experimental study of drug release kinetics showed that due to the non-covalent interactions of both simvastatin and ibuprofen sodium salt with the particles of discrete phase, prolongation of the release processes was observed.

Glycosylium Ions in Superacid Mimic the Transition State of Enzyme Reactions.

The hydrolysis of glycosides is a biochemical transformation that occurs in all living organisms, catalyzed by a broad group of enzymes, including glycoside hydrolases. These enzymes cleave the glycosidic bond via a transition state with substantial oxocarbenium ion character, resulting in short-lived oxocarbenium ion-like species. While such transient species have been inferred through theoretical studies and kinetic isotope effect measurements, their direct spectroscopic characterization remains challenging. In this study, we exploit a superacid environment to generate, accumulate, and fully characterize nonprotected 2-deoxy glycosyl cations in the d-glucopyranose, d-galactopyranose, and l-arabinofuranose series using low-temperature NMR spectroscopy, supported by DFT calculations. Additionally, QM/MM MD simulations reveal that the properties of these glycosyl cations in superacid closely resemble those within the active sites of glycosidase enzymes, particularly in terms of conformation and anomeric charge distribution. These findings highlight a parallel between the stabilizing effect of counterions in superacid media and the network of multidentate noncovalent interactions within glycosidase active sites, which stabilize transition states with pronounced oxocarbenium ion character.

Cryo-EM of human rhinovirus reveals capsid-RNA duplex interactions that provide insights into virus assembly and genome uncoating.

The cryo-EM structure of the human rhinovirus B14 determined in this study reveals 13-bp RNA duplexes symmetrically bound to regions around each of the 30 two-fold axes in the icosahedral viral capsid. The RNA duplexes (~12% of the ssRNA genome) define a quasi-dodecahedral cage that line a substantial part of the capsid interior surface. The RNA duplexes establish a complex network of non-covalent interactions with pockets in the capsid inner wall, including coulombic interactions with a cluster of basic amino acid residues that surround each RNA duplex. A direct comparison was made between the cryo-EM structure of RNA-filled virions and that of RNA-free (empty) capsids that resulted from genome release from a small fraction of viruses. The comparison reveals that some specific residues involved in capsid-duplex RNA interactions in the virion undergo remarkable conformational rearrangements upon RNA release from the capsid. RNA release is also associated with the asynchronous opening of channels at the 30 two-fold axes. The results provide further insights into the molecular mechanisms leading to assembly of rhinovirus particles and their genome uncoating during infection. They may also contribute to development of novel antiviral strategies aimed at interfering with viral capsid-genome interactions during the infectious cycle.

Quenching Rate Constants of Lewis Base-Boryl Radical by Substrates: a Laser Flash Photolysis Study.

The advanced strategy using Lewis base-boryl radicals (LBRs) has recently been proposed for the addition of alkyl substituents to the full-carbon quaternary center of an organic molecule. However, as the rate-determining step in the whole route, reaction rate constants of LBRs with substrates are extremely lacking. In this paper, 4-dimethylaminopyridine (DMAP)-BH2• was selected as a representative of LBRs, and its reactions with six monochloro-substituted substrates, including three methyl chlorobenzoates and three chlorinated acetanilides were studied in experiments and theoretical calculations. The bimolecular reaction rate constants, kq, were determined using laser flash photolysis approach. By comparing activation energies along the two addition pathways, we have clarified the rate-determining step as the attacking to carbonyl oxygen instead of chlorine atom. Furthermore, noncovalent interaction (NCI) analyses on these substrates indicate that weak interactions, such as hydrogen-bonding and van der Waals interactions, have significant influence on the reactivity of these substrates. Our study provides concrete clues to extend this synthetic strategy.

Flippingthe Metalation of 4-Dimethylaminopyridine: Steric Repulsion versusLondon Dispersion Attraction.

Non-covalent interactions, including the coordination of an organolithium reagent by a directing group and the steric hindrance from substituents, play a crucial role in determining the selectivity of metalation reactions. Here, we demonstrate the effective utilization of steric interactions for "flipping" the lithiation of 4-dimethylaminopyridine (DMAP). Introduction of a Me3Si substituent to the position 1 of DMAP or simple complexation with t-BuLi allows selective C3-lithiation, due to the steric hindrance of a C2-H bond by the bulky moiety at the pyridine nitrogen. This simple approach creates a convenient way to achieve the selective C3-functionalization of DMAP. In contrast, the utilization of an even bulkier i-Pr3Si substituent leads to exclusive C2-functionalization due to the dispersion interactions with organometallic bases. For the first time, it is demonstrated that the i-Pr3Si moiety can serve as a directing group, providing a new type of direct ortho-metalation effect.

Engaging Two Anions with Single Cation in Energetic Salts: Approach for Optimization of Oxygen Balance in Energetic Materials.

The field of high energy density materials faces a long-standing challenge to achieve an optimum balance between energy and stability. While energetic salt formation via a combination of oxygen- and nitrogen-rich anions (providing energy) with nitrogen-containing cations (providing stability) has been a proven approach for improving physical stability, constraints such as lowering density and energetic performance remain unresolved. This can be addressed by utilizing oxygen-containing cations for salt formation. However, this approach is rarely explored because its synthesis is challenging. In this work, we have designed an oxygen-rich cationic precursor 2 by incorporating 4-amino-3,5-dinitropyrazole with 3,4-diaminotriazole via an N-methylene-C bridge. Further combination with energetic acids resulted in the formation of high-performing, physically stable energetic salts 3-10. The salts were found to be generally more energetic than the salts of respective energetic acids with previously reported cations and showed prominent improvement in physical stability with respect to their anionic precursors. All the compounds were thoroughly characterized through IR, NMR spectroscopy, HRMS, and elemental analysis. Salt 9 was confirmed through 15N NMR analysis, and salts 2 and 8 were confirmed through single-crystal X-ray diffraction. Additional analyses such as Hirshfeld surface analysis, noncovalent interaction (NCI) analysis, and electrostatic potential studies were also carried out to correlate the structure-property relationship.

Amphiphilic Oligonucleotide Derivatives—Promising Tools for Therapeutics

Recent advances in genetics and nucleic acid chemistry have created fundamentally new tools, both for practical applications in therapy and diagnostics and for fundamental genome editing tasks. Nucleic acid-based therapeutic agents offer a distinct advantage of selectively targeting the underlying cause of the disease. Nevertheless, despite the success achieved thus far, there remain unresolved issues regarding the improvement of the pharmacokinetic properties of therapeutic nucleic acids while preserving their biological activity. In order to address these challenges, there is a growing focus on the study of safe and effective delivery methods utilising modified nucleic acid analogues and their lipid bioconjugates. The present review article provides an overview of the current state of the art in the use of chemically modified nucleic acid derivatives for therapeutic applications, with a particular focus on oligonucleotides conjugated to lipid moieties. A systematic analysis has been conducted to investigate the ability of amphiphilic oligonucleotides to self-assemble into micelle-like structures, as well as the influence of non-covalent interactions of such derivatives with serum albumin on their biodistribution and therapeutic effects.