Aggregation Of Small Molecules Research Articles

Ligand-Receptor Interaction-Induced Intracellular Phase Separation: A Global Disruption Strategy for Resistance-Free Lethality of Pathogenic Bacteria.

Addressing the global challenge of bacterial resistance demands innovative approaches, among which multitargeting is a widely used strategy. Current strategies of multitargeting, typically achieved through drug combinations or single agents inherently aiming at multiple targets, face challenges such as stringent pharmacokinetic and pharmacodynamic requirements and cytotoxicity concerns. In this report, we propose a bacterial-specific global disruption approach as a vastly expanded multitargeting strategy that effectively disrupts bacterial subcellular organization. This effect is achieved through a pioneering chemical design of ligand-receptor interaction-induced aggregation of small molecules, i.e., DNA-induced aggregation of a diarginine peptidomimetic within bacterial cells. These intracellular aggregates display affinity toward various proteins and thus substantially interfere with essential bacterial functions and rupture bacterial cell membranes in an "inside-out" manner, leading to robust antibacterial activities and suppression of drug resistance. Additionally, biochemical analysis of macromolecule binding affinity, cytoplasmic localization patterns, and bacterial stress responses suggests that this bacterial-specific intracellular aggregation mechanism is fundamentally different from nonselective classic DNA or membrane binding mechanisms. These mechanistic distinctions, along with the peptidomimetic's selective permeation of bacterial membranes, contribute to its favorable biocompatibility and pharmacokinetic properties, enabling its in vivo antimicrobial efficacy in several animal models, including mice-based superficial wound models, subcutaneous abscess models, and septicemia infection models. These results highlight the great promise of ligand-receptor interaction-induced intracellular aggregation in achieving a globally disruptive multitargeting effect, thereby offering potential applications in the treatment of malignant cells, including pathogens, tumor cells, and infected tissues.

Predictions of Colloidal Molecular Aggregation Using AI/ML Models.

To facilitate the triage of hits from small molecule screens, we have used various AI/ML techniques and experimentally observed data sets to build models aimed at predicting colloidal aggregation of small organic molecules in aqueous solution. We have found that Naïve Bayesian and deep neural networks outperform logistic regression, recursive partitioning tree, support vector machine, and random forest techniques by having the lowest balanced error rate (BER) for the test set. Derived predictive classification models consistently and successfully discriminated aggregator molecules from nonaggregator hits. An analysis of molecular descriptors in favor of colloidal aggregation confirms previous observations (hydrophobicity, molecular weight, and solubility) in addition to undescribed molecular descriptors such as the fraction of sp3 carbon atoms (Fsp3), and electrotopological state of hydroxyl groups (ES_Sum_sOH). Naïve Bayesian modeling and scaffold tree analysis have revealed chemical features/scaffolds contributing the most to colloidal aggregation and nonaggregation, respectively. These results highlight the importance of scaffolds with high Fsp3 values in promoting nonaggregation. Matched molecular pair analysis (MMPA) has also deciphered context-dependent substitutions, which can be used to design nonaggregator molecules. We found that most matched molecular pairs have a neutral effect on aggregation propensity. We have prospectively applied our predictive models to assist in chemical library triage for optimal plate selection diversity and purchase for high throughput screening (HTS) in drug discovery projects.

Molecular dynamics simulations as a guide for modulating small molecule aggregation

Small colloidally aggregating molecules (SCAMs) can be problematic for biological assays in drug discovery campaigns. However, the self-associating properties of SCAMs have potential applications in drug delivery and analytical biochemistry. Consequently, the ability to predict the aggregation propensity of a small organic molecule is of considerable interest. Chemoinformatics-based filters such as ChemAGG and Aggregator Advisor offer rapid assessment but are limited by the assay quality and structural diversity of their training set data. Complementary to these tools, we explore here the ability of molecular dynamics (MD) simulations as a physics-based method capable of predicting the aggregation propensity of diverse chemical structures. For a set of 32 molecules, using simulations of 100 ns in explicit solvent, we find a success rate of 97% (one molecule misclassified) as opposed to 75% by Aggregator Advisor and 72% by ChemAGG. These short timescale MD simulations are representative of longer microsecond trajectories and yield an informative spectrum of aggregation propensities across the set of solutes, capturing the dynamic behaviour of weakly aggregating compounds. Implicit solvent simulations using the generalized Born model were less successful in predicting aggregation propensity. MD simulations were also performed to explore structure-aggregation relationships for selected molecules, identifying chemical modifications that reversed the predicted behaviour of a given aggregator/non-aggregator compound. While lower throughput than rapid cheminformatics-based SCAM filters, MD-based prediction of aggregation has potential to be deployed on the scale of focused subsets of moderate size, and, depending on the target application, provide guidance on removing or optimizing a compound’s aggregation propensity.Graphical

Under the microscope: A structural and mechanistic examination of novel tau-targeted small-molecule aggregation inhibitors

Under the microscope: A structural and mechanistic examination of novel tau-targeted small-molecule aggregation inhibitors

Expulsion of small molecule hydrocarbons and expansion of nanopores effect in tectonically deformed coal evolution

This work aimed to investigate the impact of the evolution of small molecular structures during the deformation of coal on the constraints imposed on nanoscale pores and adsorption behaviors. Both undeformed and tectonically deformed coal (TDC) from the Huaibei mining area in China were collected for analysis. The pyridine was employed for the extraction of small molecules from coal, which was further complemented by Fourier-transform infrared spectroscopy (FTIR) and low-pressure CO2 and N2 adsorption experiments (LP-CO2/N2AD). The study yielded the following results: (1) Intense tectonic stresses facilitate the removal and recombination of small molecular side chains within the basic structural units (BSU) of coal. As deformation occurs, hydroxyl groups, aliphatic hydrocarbons, C=O, C=C, aromatic hydrocarbons, and 'C' structures tend to accumulate, resulting in an enhanced extraction rate. (2) The deformation process of the coal demonstrates a significant pore-expansion effect, with the most substantial increase observed in micropores (surface area increased by over 70 %), followed by mesopores and macropores. This enlargement facilitates the aggregation of small molecules and gas storage. (3) Intense deformation stages involving shear slip, ductile deformation, and maceral fragmentation result in small molecular fractures and an increased number of micropores. The removal and recombination of I, DOC, and CH2/CH3 within BSUs lead to the formation of larger interconnected pores accompanied by the aggregation of hydroxyl groups (OH–), C=O, C=C, aliphatic hydrocarbons, and 'C' structures. (4) The adsorption capacity of residual coal is lower than that of the raw coal before extraction, indicating that small molecular structures contribute to increased adsorption. This likely plays a significant role in the higher gas content observed in structurally deformed coal. The removal of small molecular structures effectively diminishes the adsorption capacity, providing novel perspectives for coalbed methane development and gas extraction in TDC areas.

Molecular dynamics and kinetics of isothermal cold crystallization with tunable dimensionality in a molecular glass former, 5'-(2,3-difluorophenyl)-2'-ethoxy-4-pentyloxy-2,3-difluorotolane.

This paper characterizes the molecular mobility that triggers the cold crystallization abilities in 5'-(2,3-difluorophenyl)-2'-ethoxy-4-pentyloxy-2,3-difluorotolane (short name DFP25DFT) material by broadband dielectric spectroscopy (BDS). We analyze the properties of identified molecular motions by referring to the Vogel-Fulcher-Tammann (VFT) model for the structural α-process associated with molecular rotation in isotropic liquid and the Eyring and Starkweather approach for the thermally activated processes, β-process related to intramolecular movement in liquid and glassy state and emerging during cold crystallization α'-process ascribed to confined movements of molecules located adjacent to crystalline surfaces. To characterize the material, we employ single-crystal X-ray diffraction, differential scanning calorimetry (DSC), adiabatic calorimetry, and polarizing optical microscopy (POM), while we utilize molecular mechanics simulations (MM2) to explore molecular flexibility. Our study focuses on inter- and intramolecular interactions that determine the cold-crystallization tendency. We demonstrate that the solidification path is controlled by the fragility of the system, the dipole-dipole attraction, and the intramolecular dynamics. The study of cold crystallization kinetics under isothermal conditions reveals the complexity of the process: the formation of two crystalline phases, Cr2 and Cr3, proceeding in different modes. This feature discloses the possibility of switching the crystal growth between three- and two-dimensional in the cold-crystallization process driven by different mechanisms.

Combating small-molecule aggregation with machine learning

Biological screens are plagued by false-positive hits resulting from aggregation. Methods to triage small colloidally aggregating molecules (SCAMs) are in high demand. Herein, we disclose a neural network to flag such entities. Our data demonstrate the utility of machine learning for predicting SCAMs, achieving 80% of correct predictions in an out-of-sample evaluation. The tool is competitive with a panel of expert chemists, who correctly predict 61% ± 7% of the same molecules in a Turing-like test. Our computational routine provides insight into features governing aggregation that had remained hidden to expert intuition. Further, we quantify that up to 15%–20% of ligands in publicly available chemogenomic databases have high potential to aggregate at a typical screening concentration (30 μM), imposing caution in systems biology and drug design programs. Our approach provides a means to augment human intuition and mitigate attrition and a pathway to accelerate future molecular medicine.

Mobility of Small Molecules in Solid Polymer Film for π-Stacked Crystallization

Crystallization or π-stacked aggregation of small molecules is an extensively observed phenomenon which favors charge transport along the crystal axis and is important for the design of organic optoelectronic devices. Such a process has been reported for N,N′-Bis(1-ethylpropyl)-3,4,9,10-perylenebis(dicarboximide) (EPPTC). However, the π-stacking mechanism requires solution–air or solution–solid interfaces. The crystallization or aggregation of molecules doped in solid films is generally thought to be impossible, since the solid environment surrounding the small molecules does not allow them to aggregate together into π-stacked crystals. In this work, we demonstrate that the movement of the EPPTC molecules becomes possible in a solid polymer film when it is heated to above the glass transition temperature of the polymer. Thus, crystal particles can be produced as a doped matrix in a thin solid film. The crystallization process is found to be strongly dependent on the annealing temperature and the annealing time. Both the microscopic and spectroscopic evaluations verify such discoveries and characterize the related properties of these crystals.

Snapshots into carbon dots formation through a combined spectroscopic approach

The design of novel carbon dots with ad hoc properties requires a comprehensive understanding of their formation mechanism, which is a complex task considering the number of variables involved, such as reaction time, structure of precursors or synthetic protocol employed. Herein, we systematically investigated the formation of carbon nanodots by tracking structural, chemical and photophysical features during the hydrothermal synthesis. We demonstrate that the formation of carbon nanodots consists of 4 consecutive steps: (i) aggregation of small organic molecules, (ii) formation of a dense core with an extended shell, (iii) collapse of the shell and (iv) aromatization of the core. In addition, we provide examples of routes towards tuning the core-shell design, synthesizing five novel carbon dots that all consist of an electron-dense core covered by an amine rich ligand shell.

Study on formation mechanism of three types of carbon nanoparticles during ethylene pyrolysis in thermal plasmas

Products of three carbon phases were synthesized by the pyrolysis of ethylene using a magnetically rotating arc under atmospheric pressure; the products thus produced were graphene nanoflakes, semi-graphite particles, and carbon nanospheres. The effects of temperature, buffer gas flow and gas type (H2 and CO2), and high temperature residence time on the morphology of the products were investigated. The results revealed that a higher temperature, proper H2 and CO2 flow, and a shorter residence time are favorable for the production of graphene with fewer layers, fewer defects, and higher purity. A suitable H/C ratio and the formation of macromolecular carbonaceous clusters are essential factors for the synthesis of semi-graphite particles. The overgrowth of graphene and the aggregation of small molecules of PAHs in the low temperature region are favorable for the formation of carbon nanospheres.

Fluorescence in "Nonfluorescent" Polymers.

Recently, a great deal of research has been started on generating fairly strong photoluminescence from organic molecules without having any conjugated π-system or fluorophore. Discrete chromophores or auxochromophores termed as “subfluorophores” may undergo “space conjugation” via co-operative intramolecular conformation followed by intermolecular aggregation to generate fluorescence or sometimes phosphorescence emission. Polymeric materials are important in this regard as nonconjugated polymers self-assemble/aggregate in a moderately concentrated solution and also in the solid state, producing membranes, films, and so forth with good physical and mechanical properties. Therefore, promoting fluorescence in these commodity polymers is very much useful for sensing, organic light emitting diodes (OLED), and biological applications. In this perspective, we have discussed the aggregation-induced emission from four different types of architectures, for example, (i) dendrimers or hyperbranched polymers, (ii) entrapped polymeric micellar self-assembly, (iii) cluster formation, and (iv) stretching-induced aggregation, begining with the genesis of fluorescence from aggregation of propeller-shaped small organic molecules. The mechanism of induced fluorescence of polymers with subfluorophoric groups is also discussed from the theoretical calculations of the energy bands in the aggregated state. Also, an attempt has been made to highlight some useful applications in the sensing of surfactants, bacteria, cell imaging, drug delivery, gene delivery, OLED, and so forth.

Differently Linked Perylene Bisimide Dimers with Various Twisting and Phase Structures for Nonfullerene All-Small-Molecule Organic Solar Cells

Nonfullerene all-small-molecule organic solar cells (NF all-SMSCs) are an important classification in the organic solar cell system. However, the application and research of NF all-SMSCs are limited due to the easy aggregation of small molecules to form large-phase domains. Perylene bisimides (PBIs) have been widely used as nonfullerene acceptors. Simply changing the link position of the PBI dimer can control the accumulation of molecules to regulate the size of the phase domain. Herein, the bay-linked, ortho-linked, and hydrazine-linked PBI dimers as nonfullerene acceptors, named as B-SdiPBI, O-SdiPBI, and H-SdiPBI, respectively, were chosen. The link position of the PBI dimer can lead to diverse molecular torsion and planarity, which affects the film-forming ability, phase separation, and thus optoelectronic properties. NF all-SMSCs based on B-SdiPBI, O-SdiPBI, and H-SdiPBI as nonfullerene acceptors and a small molecule DR3TBDTT as the donor achieve the best power conversion efficiencies of 1.93, 3.30, and 4.05%, respectively. The result is consistent with the sequence of inter-PBI twist and phase domain size of the corresponding blend films in the device. The DR3TBDTT:H-SdiPBI system has the best efficiency with the largest dihedral angle of H-SdiPBI (ψ = 90°) and an appropriate phase size (10–40 nm), whereas the smaller dihedral angle of O-SdiPBI (ψ = 86°) produces a larger phase size (20–50 nm) and the smallest dihedral angle of B-SdiPBI (ψ = 71°) gives the largest phase size (30–80 nm). This illustrates that the twist angle can effectively increase the phase separation between the acceptor and donor to obtain an effective phase size in this system. The work provides a guide for designing the acceptors and controlling phase domains of high-performance NF all-SMSCs.

Supramolecular Polymers – we've Come Full Circle

AbstractSince the first polymers were discovered, scientists have debated their structures. Before Hermann Staudinger published the brilliant concept of macromolecules, polymer properties were generally believed to be based on the colloidal aggregation of small particles or molecules. From 1920 onwards, polymers and macromolecules are synonymous with each other; i. e. materials made by many covalent bonds connecting monomers in 2 or 3 dimensions. Although supramolecular interactions between macromolecular chains are evidently important, e. g. in nylons, it was unheard of to proposing polymeric materials based on the interaction of small molecules. Breakthroughs in supramolecular chemistry, however, showed that polymer materials can be made by small molecules using strong directional secondary interactions; the field of supramolecular polymers emerged. In a way, we have come full circle. In this essay we give a personal story about the birth of supramolecular polymers, with special emphasis on their structures, way of formation, and the dynamic nature of their bonding. The adaptivity of supramolecular polymers has become a major asset for novel applications, e. g. in the direction for the sustainable use of polymers, but also in biomedicine and electronics as well as self‐healing materials. The lessons learned in the past years include aspects that forecast a bright future for the use of supramolecular interactions in polymer materials in general and for supramolecular polymers in particular. In order to give full tribute to Staudinger in the year celebrating 100 years of macromolecules, we will show that many of the concepts of macromolecular polymers apply to supramolecular polymers, with only one important difference with fascinating consequences: the dynamic nature of the bonds that form polymer chains.

Atomistic simulations of the aggregation of small aromatic molecules in homogenous and heterogenous mixtures.

The relatively weak London dispersion forces are the only interactions that could cause aggregation between simple aromatic molecules. The use of molecular dynamics and high-level ab initio computer simulations has been used to describe the aggregation and interactions between molecular systems containing benzene, naphthalene and anthracene. Mixtures containing one type of molecule (homogenous) and more than one type of molecule (heterogenous) were considered. Our results indicate that as molecular weight increases so does the temperature at which aggregation will occur. In all simulations, the mechanism of aggregation is through small clusters coalescing into larger clusters. The structural analysis of the molecules within the clusters reveals that benzene will orient itself in T-shaped and parallel displaced configurations. Molecules of anthracene prefer to orient themselves in a similar manner to a bulk crystal with no T-shaped configuration observed. The aggregation of these aromatic molecules is discussed in the context of astrochemistry with particular reference to the dust formation region around stars.

100 Years of Macromolecular Science

100 Years of Macromolecular Science

Lipid Membranes Influence the Ability of Small Molecules To Inhibit Huntingtin Fibrillization.

Several diseases, including Alzheimer's disease, Parkinson's disease, and Huntington's disease (HD), are associated with specific proteins aggregating and depositing within tissues and/or cellular compartments. The aggregation of these proteins is characterized by the formation of extended, β-sheet rich fibrils, termed amyloid. In addition, a variety of other aggregate species also form, including oligomers and protofibrils. Specifically, HD is caused by the aggregation of the huntingtin (htt) protein that contains an expanded polyglutamine domain. Due to the link between protein aggregation and disease, small molecule aggregation inhibitors have been pursued as potential therapeutic agents. Two such small molecules are epigallocatechin 3-gallate (EGCG) and curcumin, both of which inhibit the fibril formation of several amyloid-forming proteins. However, amyloid formation is a complex process that is strongly influenced by the protein's environment, leading to distinct aggregation pathways. Thus, changes in the protein's environment may alter the effectiveness of aggregation inhibitors. A well-known modulator of amyloid formation is lipid membranes. Here, we investigated if the presence of lipid vesicles altered the ability of EGCG or curcumin to modulate htt aggregation and influence the interaction of htt with lipid membranes. The presence of 1-palmitoyl-2-oleoyl-glycero-3-phosphocholine or total brain lipid extract vesicles prevented the curcumin from inhibiting htt fibril formation. In contrast, EGCG's inhibition of htt fibril formation persisted in the presence of lipids. Collectively, these results highlight the complexity of htt aggregation and demonstrate that the presence of lipid membranes is a key modifier of the ability of small molecules to inhibit htt fibril formation.

Protein Stability Effects in Aggregate-Based Enzyme Inhibition.

Small-molecule aggregates are a leading cause of artifacts in early drug discovery, but little is known about their interactions with proteins, nor why some proteins are more susceptible to inhibition than others. A possible reason for this apparent selectivity is that aggregation-based inhibition, as a stoichiometric process, is sensitive to protein concentration, which varies across assays. Alternatively, local protein unfolding by aggregates may lead to selectivity since stability varies among proteins. To deconvolute these effects, we used differentially stable point mutants of a single protein, TEM-1 β-lactamase. Broadly, destabilized mutants had higher affinities for and were more potently inhibited by aggregates versus more stable variants. The addition of the irreversible inhibitor moxalactam destabilized several mutants, and these typically bound tighter to a colloidal particle, while the only mutant it stabilized bound weaker. These results suggest that less-stable enzymes are more easily sequestered and inhibited by colloidal aggregates.

A Computational Predictive Approach for Controlling the Morphology of Functional Molecular Aggregates on Substrates

AbstractFull control of the growth dynamics and morphology of nanoscale molecular aggregates on substrates is a crucial factor for the development of novel materials and devices for technological applications. A novel computational approach based on molecular dynamics, which is able to predict the structure of nanoscale aggregates of organic small molecules on substrates as a function of growth and processing conditions, is presented. In the simulation protocol proposed, molecules are progressively added to the substrate, one by one, reproducing vacuum thermal deposition processes. The simulation parameters affect the structure of the configuration, and formation of molecular aggregates is spontaneously observed upon reaching a critical molecular density at the interface. Suitable simulation parameters allow to access different molecular aggregation morphologies on substrates, including crystalline phases, matching the structural variability observed in real fabrication conditions. This approach is benchmarked by simulating the morphology of aggregates of N,N′‐ditridecylperylene‐3,4,9,10‐tetracarboxylic diimide (PTCDI‐C13), a prototypical n‐type semiconductor for organic electronics, on graphene, in different growth conditions. Simulations predict structural features of aggregates of PTCDI‐C13 on graphene that are in excellent agreement with experiments and, at the same time, provide a rationale and quantitative relationship between molecular structure and observed aggregation morphologies.

Organic Fluorescent Dye-based Nanomaterials: Advances in the Rational Design for Imaging and Sensing Applications.

Self-assembled fluorescent nanomaterials based on small-molecule organic dyes are gaining increasing popularity in imaging and sensing applications over the past decade. This is primarily due to their ability to combine spectral properties tunability and biocompatibility of small molecule organic fluorophores with brightness, chemical and colloidal stability of inorganic materials. Such a unique combination of features comes with rich versatility of dye-based nanomaterials: from aggregates of small molecules to sophisticated core-shell nanoarchitectures involving hyperbranched polymers. Along with the ongoing discovery of new materials and better ways of their synthesis, it is very important to continue systematic studies of fundamental factors that regulate the key properties of fluorescent nanomaterials: their size, polydispersity, colloidal stability, chemical stability, absorption and emission maxima, biocompatibility, and interactions with biological interfaces. In this review, we focus on the systematic description of various types of organic fluorescent nanomaterials, approaches to their synthesis, and ways to optimize and control their characteristics. The discussion is built on examples from reports on recent advances in the design and applications of such materials. Conclusions made from this analysis allow a perspective on future development of fluorescent nanomaterials design for biomedical and related applications.

Small-Molecule Amyloid Beta-Aggregation Inhibitors in Alzheimer's Disease Drug Development

AbstractAlzheimer's disease (AD) is still an incurable neurodegenerative disease that causes dementia. AD changes the brain function that, over time, impairs memory and diminishes judgment and reasoning ability. Pathophysiology of AD is complex. Till now the cause of AD remains unknown, but risk factors include family history and genetic predisposition. The drugs previously approved for AD treatment do not modify the disease process and only provide symptomatic improvement. Over the past few decades, research has led to significant progress in the understanding of the disease, leading to several novel strategies that may modify the disease process. One of the major developments in this direction is the amyloid β (Aβ) aggregation. Small molecules could block the initial stages of Aβ aggregation, which could be the starting point for the design and development of new AD drugs in the near future. In this review we summarize the most promising small-molecule Aβ-aggregation inhibitors including natural compounds, novel small molecules, and also those are in clinical trials. Moreover, we briefly summarized some reported docking studies of small-molecule Aβ aggregation inhibitors. These will give us an idea about the chemical features required to design novel small molecules with anti-Aβ aggregation properties.