Principles Of Molecular Recognition Research Articles

Supramolecular cyclodextrin complexes of biologically active nitrogen heterocycles

The review is devoted to the rapidly developing field of modern supramolecular chemistry - cyclodextrin complexes of biologically active nitrogen heterocycles, such as piperidines, piperazines, morpholines and pyridines. Interest in cyclodextrin complexes is growing due to the search and construction of supramolecular assemblies for targeted drug delivery. The latter is achieved as a result of supramolecular self-assembly, based on the principles of molecular recognition, and is one of the areas of modern chemistry, leading to the creation of new materials with new properties. This review fully demonstrates the ongoing scientific and practical interest in the problem of encapsulation with cyclodextrins, including nanoencapsulation. Encapsulation with cyclodextrins provides a wide range of advantages: obtaining solid dosage forms from liquid ones, stabilizing and protecting active substances from the adverse effects of external factors, increasing solubility, increasing bioavailability, reducing toxicity, prolonging action, etc. The presented review includes recent advances in the field of supramolecular complexes of biologically active nitrogen heterocycles with cyclodextrins and concludes with a discussion and identification of future promising directions for research. The review presents the results of supramolecular self-assembly of biologically active azaheterocycles with cyclodextrins.

Molecular Hosts for the Sensing and Separation of 99TcO4.

In recent years, European Union member states have hastened energy policy deliberations to address supply and sustainability concerns, placing a significant emphasis on nuclear energy as a means to achieve decarbonization goals. However, despite its significant role in power generation, nuclear energy faces significant challenges linked to fuel reprocessing and waste disposal, that hinder its broader expansion. In this context, the separation of technetium represents a concerning issue. Indeed, technetium's catalytic activity can impede the extraction of uranium, neptunium, and plutonium, affecting waste reprocessing efficiency. Additionally, the stable form of technetium in aerobic conditions, pertechnetate (TcO4 -), poses risks of groundwater contamination due to its mobility and solubility. Hence, sensing and separation of TcO4 - is imperative for both nuclear fuel processing and minimising radioactive contamination in the environment. However, the binding of TcO4 - and its separation from contaminated solutions present challenges due to the acidic (or basic) waste components and the high ionic strength in real matrices. Supramolecular chemists have addressed these issues by designing receptors inspired by molecular recognition principles. This article explores recent advancements and future directions in TcO4 - sensing and separation (using extraction and sorption) with a focus on molecular hosts. Metal-organic receptors will also be discussed.

Large-scale chemoproteomics expedites ligand discovery and predicts ligand behavior in cells.

Chemical modulation of proteins enables a mechanistic understanding of biology and represents the foundation of most therapeutics. However, despite decades of research, 80% of the human proteome lacks functional ligands. Chemical proteomics has advanced fragment-based ligand discovery toward cellular systems, but throughput limitations have stymied the scalable identification of fragment-protein interactions. We report proteome-wide maps of protein-binding propensity for 407 structurally diverse small-molecule fragments. We verified that identified interactions can be advanced to active chemical probes of E3 ubiquitin ligases, transporters, and kinases. Integrating machine learning binary classifiers further enabled interpretable predictions of fragment behavior in cells. The resulting resource of fragment-protein interactions and predictive models will help to elucidate principles of molecular recognition and expedite ligand discovery efforts for hitherto undrugged proteins.

Advancements and strategic approaches in catenane synthesis.

Catenanes, a distinctive category of mechanically interlocked molecules composed of intertwined macrocycles, have undergone significant advancements since their initial stages characterized by inefficient statistical synthesis methods. Through the aid of molecular recognition processes and principles of self-assembly, a diverse array of catenanes with intricate structures can now be readily accessed utilizing template-directed synthetic protocols. The rapid evolution and emergence of this field have catalyzed the design and construction of artificial molecular switches and machines, leading to the development of increasingly integrated functional systems and materials. This review endeavors to explore the pivotal advancements in catenane synthesis from its inception, offering a comprehensive discussion of the synthetic methodologies employed in recent years. By elucidating the progress made in synthetic approaches to catenanes, our aim is to provide a clearer understanding of the future challenges in further advancing catenane chemistry from a synthetic perspective.

Structure of the photoreceptor synaptic assembly of the extracellular matrix protein pikachurin with the orphan receptor GPR179.

Precise synapse formation is essential for normal functioning of the nervous system. Retinal photoreceptors establish selective contacts with bipolar cells, aligning the neurotransmitter release apparatus with postsynaptic signaling cascades. This involves transsynaptic assembly between the dystroglycan-dystrophin complex on the photoreceptor and the orphan receptor GPR179 on the bipolar cell, which is mediated by the extracellular matrix protein pikachurin (also known as EGFLAM). This complex plays a critical role in the synaptic organization of photoreceptors and signal transmission, and mutations affecting its components cause blinding disorders in humans. Here, we investigated the structural organization and molecular mechanisms by which pikachurin orchestrates transsynaptic assembly and solved structures of the human pikachurin domains by x-ray crystallography and of the GPR179-pikachurin complex by single-particle, cryo-electron microscopy. The structures reveal molecular recognition principles of pikachurin by the Cache domains of GPR179 and show how the interaction is involved in the transsynaptic alignment of the signaling machinery. Together, these data provide a structural basis for understanding the synaptic organization of photoreceptors and ocular pathology.

Nanotechnology in Medical Field

Abstract: Nanotechnology is the field of using the technology and science that focuses on using molecular level regulation of matter that are of size range less than 100 nm range. In the field of nanotechnology, there are two primary approaches. The two main approaches are “Top-down” approach and “Bottom-up” approach. With a “Bottom-up” approach, materials and gadgets made of molecules that chemically put themselves together using molecular recognition principles are used. The nano-objects are created from larger entities using “Top-down” approach without atomic-level control. In fact, nanotechnology has been useful in a variety of medical fields, including cardiovascular medicine, oncology and the treatment of other chronic illnesses, as there is a significant need for the creation of pharmaceuticals and because the biological elements of live cells play crucial functions at the nanoscale. Undoubtedly, nanotechnology is being utilised to improve the identification of biomarkers, medication development, drug delivery and molecular diagnostics, all of which may be useful in the treatment of these patients. The imp

IRAA: A statistical tool for investigating a protein-protein interaction interface from multiple structures.

Understanding protein-protein interactions (PPIs) is fundamental to infer how different molecular systems work. A major component to model molecular recognition is the buried surface area (BSA), that is, the area that becomes inaccessible to solvent upon complex formation. To date, many attempts tried to connect BSA to molecular recognition principles, and in particular, to the underlying binding affinity. However, the most popular approach to calculate BSA is to use a single (or in some cases few) bound structures, consequently neglecting a wealth of structural information of the interacting proteins derived from ensembles corresponding to their unbound and bound states. Moreover, the most popular method inherently assumes the component proteins to bind as rigid entities. To address the above shortcomings, we developed a Monte Carlo method-based Interface Residue Assessment Algorithm (IRAA), to calculate a combined distribution of BSA for a given complex. Further, we apply our algorithm to human ACE2 and SARS-CoV-2 Spike protein complex, a system of prime importance. Results show a much broader distribution of BSA compared to that obtained from only the bound structure or structures and extended residue members of the interface with implications to the underlying biomolecular recognition. We derive that specific interface residues of ACE2 and of S-protein are consistently highly flexible, whereas other residues systematically show minor conformational variations. In effect, IRAA facilitates the use of all available structural data for any biomolecular complex of interest, extracting quantitative parameters with statistical significance, thereby providing a deeper biophysical understanding of the molecular system under investigation.

Metabolite-Responsive Liposomes Employing Synthetic Lipid Switches Driven by Molecular Recognition Principles.

The ability to exert control over lipid properties, including structure, charge, function, and self-assembly characteristics is a powerful tool that can be implemented to achieve a wide range of biomedical applications. Examples in this arena include the development of caged lipids for controlled activation of signaling properties, metabolic labeling strategies for tracking lipid biosynthesis, lipid activity probes for identifying cognate binding partners, approaches for in situ membrane assembly, and liposome triggered release strategies. In this Account, we describe recent advancements in the latter area entailing the development of stimuli-responsive liposomes through programmable changes to lipid self-assembly properties, which can be harnessed to drive the release of encapsulated contents toward applications including drug delivery. We will focus on an emerging paradigm involving liposomal platforms that are sensitized toward chemical agents ranging from metal cations to small organic molecules that exhibit dysregulation in disease states. This has been achieved by developing synthetic lipid switches that are designed to undergo programmed conformational changes upon the recognition of specific target analytes. These structural alterations are leveraged to perturb the packing of lipids within the membrane and thereby drive the release of encapsulated contents.We provide an overview of the inspiration, design, and characterization of liposomes that selectively respond to wide-ranging target analytes. This series of studies began with the development of calcium-responsive liposomes utilizing a lipid switch inspired by sensors including indo-1. Following this successful demonstration, we next showed that the selectivity of the lipid switch could be altered among different metal cations by producing a liposomal platform for which release is induced through zinc binding. Our next goal was to develop metabolite-responsive liposomes in which switching is driven by molecular recognition events involving phosphorylated small molecules. In this work, screening of lipid switches designed to interact with phosphorylated metabolites led to the identification of liposomal formulations that selectivity release contents in the presence of adenosine triphosphate (ATP). Finally, we were able to modulate the metabolite selectivity by rationally designing a modified lipid switch structure that is activated through complexation of inositol-(1,4,5)-trisphosphate (IP3). These projects show the progression of our approaches for liposome release triggered by molecular recognition principles, building from ion-responsive lipid switches to structures that are activated by small molecules. These "smart" liposomal platforms provide an important addition to the toolbox for controlled cargo release since they respond to ions or small molecules that are commonly overproduced by diseased cells.

Features of the Supramolecular Cell-Genetic Organization of E. Coli in Engineering Aspects of Biotechnology

Recently, there has been a keen interest in the physicochemical features of self-organizing spatio-temporal, heteropolymer-supramolecular assemblies, in which the system of components of the fluctuation dynamics of surface protein groups is evolutionarily selected for the implementation of morphogenetic processes of ontogenesis.That is, evolution created chemical compounds, the exceptional organization of which ensured the fulfillment of the most complex and precise tasks.In this research, the bacterial cell ofE. coli was considered in the concept of supramolecular science, where, in accordance with the informational development program based on the principles of molecular recognition, phase ensembles appear, which are characterized by a certain organization, depending on the phase growth of the population culture. In this respect, proteomic super-molecular physicochemistry can be considered as physicochemical or molecular informatics.Arginine is of interest because almost all of its molecule is active and undergoes obligatory interactions both with DNA and with other histones and non-histones. The results of this study demonstrated the super-protein surface of supramolecular assemblies, the flexible system PPCС-E.coli, active zones, dynamics of continuity, positioning topologicalspatio-temporal Arg-protease-processing, local areas of the nucleoid system, and interrelations at the level of: Bp-liquid crystal-bacterioplasma; NsCo-fragile, PsCo-tightly bound to the cell remainder; and in the Co-cell remainder itself. These data may be of practical interest in various engineering aspects of biotechnology.
 Keywords: arginine protease processing, supramolecules, E.coli, phase protein, super-molecules.

Geometrical and electro-static determinants of protein-protein interactions.

Protein-protein interactions (PPI) are pivotal to the numerous processes in the cell. Therefore, it is of interest to document the analysis of these interactions in terms of binding sites, topology of the interacting structures and physiochemical properties of interacting interfaces and the of forces interactions. The interaction interface of obligatory protein-protein complexes differs from that of the transient interactions. We have created a large database of protein-protein interactions containing over100 thousand interfaces. The structural redundancy was eliminated to obtain a non-redundant database of over 2,265 interaction interfaces. Therefore, it is of interest to document the analysis of these interactions in terms of binding sites, topology of the interacting structures and physiochemical properties of interacting interfaces and the offorces interactions. The residue interaction propensity and all of the rest of the parametric scores converged to a statistical indistinguishable common sub-range and followed the similar distribution trends for all three classes of sequence-based classifications PPInS. This indicates that the principles of molecular recognition are dependent on the preciseness of the fit in the interaction interfaces. Thus, it reinforces the importance of geometrical and electrostatic complementarity as the main determinants for PPIs.

Structural Profiling of Bacterial Effectors Reveals Enrichment of Host-Interacting Domains and Motifs.

Effector proteins are bacterial virulence factors secreted directly into host cells and, through extensive interactions with host proteins, rewire host signaling pathways to the advantage of the pathogen. Despite the crucial role of globular domains as mediators of protein-protein interactions (PPIs), previous structural studies of bacterial effectors are primarily focused on individual domains, rather than domain-mediated PPIs, which limits their ability to uncover systems-level molecular recognition principles governing host-bacteria interactions. Here, we took an interaction-centric approach and systematically examined the potential of structural components within bacterial proteins to engage in or target eukaryote-specific domain-domain interactions (DDIs). Our results indicate that: 1) effectors are about six times as likely as non-effectors to contain host-like domains that mediate DDIs exclusively in eukaryotes; 2) the average domain in effectors is about seven times as likely as that in non-effectors to co-occur with DDI partners in eukaryotes rather than in bacteria; and 3) effectors are about nine times as likely as non-effectors to contain bacteria-exclusive domains that target host domains mediating DDIs exclusively in eukaryotes. Moreover, in the absence of host-like domains or among pathogen proteins without domain assignment, effectors harbor a higher variety and density of short linear motifs targeting host domains that mediate DDIs exclusively in eukaryotes. Our study lends novel quantitative insight into the structural basis of effector-induced perturbation of host-endogenous PPIs and may aid in the design of selective inhibitors of host-pathogen interactions.

A Global Map of G Protein Signaling Regulation by RGS Proteins

SummaryThe control over the extent and timing of G protein signaling is provided by the regulator of G protein signaling (RGS) proteins that deactivate G protein α subunits (Gα). Mammalian genomes encode 20 canonical RGS and 16 Gα genes with key roles in physiology and disease. To understand the principles governing the selectivity of Gα regulation by RGS, we examine the catalytic activity of all canonical human RGS proteins and their selectivity for a complete set of Gα substrates using real-time kinetic measurements in living cells. The data reveal rules governing RGS-Gα recognition, the structural basis of its selectivity, and provide principles for engineering RGS proteins with defined selectivity. The study also explores the evolution of RGS-Gα selectivity through ancestral reconstruction and demonstrates how naturally occurring non-synonymous variants in RGS alter signaling. These results provide a blueprint for decoding signaling selectivity and advance our understanding of molecular recognition principles.

Understanding the Contributions of Conformational Changes, Thermodynamics, and Kinetics of RNA-Small Molecule Interactions.

The implication of RNA in multiple cellular processes beyond protein coding has revitalized interest in the development of small molecules for therapeutically targeting RNA and for further probing its cellular biology. However, the process of rationally designing such small molecule probes is hampered by the paucity of information about fundamental molecular recognition principles of RNA. In this Review, we summarize two important and often underappreciated aspects of RNA-small molecule recognition: RNA conformational dynamics and the biophysical properties of interactions of small molecules with RNA, specifically thermodynamics and kinetics. While conformational flexibility is often said to impede RNA ligand development, the ability of small molecules to influence the RNA conformational landscape can have a significant effect on the cellular functions of RNA. An analysis of the conformational landscape of RNA and the interactions of individual conformations with ligands can thus guide the development of new small molecule probes, which needs to be investigated further. Additionally, while it is common practice to quantify the binding affinities ( Ka or Kd) of small molecules for biomacromolecules as a measure of their activity, further biophysical characterization of their interaction can provide a deeper understanding. Studies that focus on the thermodynamic and kinetic parameters for interaction between RNA and ligands are next discussed. Finally, this Review provides the reader with a perspective on how such in-depth analysis of biophysical characteristics of the interaction of RNA and small molecules can impact our understanding of these interactions and how they will benefit the future design of small molecule probes.

Structural motifs in eIF4G and 4E-BPs modulate their binding to eIF4E to regulate translation initiation in yeast.

The interaction of the eukaryotic initiation factor 4G (eIF4G) with the cap-binding protein eIF4E initiates cap-dependent translation and is regulated by the 4E-binding proteins (4E-BPs), which compete with eIF4G to repress translation. Metazoan eIF4G and 4E-BPs interact with eIF4E via canonical and non-canonical motifs that bind to the dorsal and lateral surface of eIF4E in a bipartite recognition mode. However, previous studies pointed to mechanistic differences in how fungi and metazoans regulate protein synthesis. We present crystal structures of the yeast eIF4E bound to two yeast 4E-BPs, p20 and Eap1p, as well as crystal structures of a fungal eIF4E–eIF4G complex. We demonstrate that the core principles of molecular recognition of eIF4E are in fact highly conserved among translational activators and repressors in eukaryotes. Finally, we reveal that highly specialized structural motifs do exist and serve to modulate the affinity of protein-protein interactions that regulate cap-dependent translation initiation in fungi.

Calcium-Responsive Liposomes via a Synthetic Lipid Switch.

Liposomal drug delivery would benefit from enhanced control over content release. Here, we report a novel avenue for triggering release driven by chemical composition using liposomes sensitized to calcium-a target chosen due to its key roles in biology and disease. To demonstrate this principle, we synthesized calcium-responsive lipid switch 1, designed to undergo conformational changes upon calcium binding. The conformational change perturbs membrane integrity, thereby promoting cargo release. This was shown through fluorescence-based release assays via dose-dependent response depending on the percentage of 1 in liposomes, with minimal background leakage in controls. DLS experiments indicated dramatic changes in particle size upon treatment of liposomes containing 1 with calcium. In a comparison of ten naturally occurring metal cations, calcium provided the greatest release. Finally, STEM images showed significant changes in liposome morphology upon treatment of liposomes containing 1 with calcium. These results showcase lipid switches driven by molecular recognition principles as an exciting avenue for controlling membrane properties.

AIE-active bis-cyanostilbene-based organogels for quantitative fluorescence sensing of CO2 based on molecular recognition principles

Fluorescence sensing of CO2 is achieved by the use of gel aggregates and xerogel systems made with the aggregation induced emissive bis-cyanostilbene derivative 1 reaching a detection limit as low as 4.5 ppm.

A Bioorganic Chemistry Approach to Understanding Molecular Recognition in Protein–Nucleic Acid Complexes

Abstract A combination of synthetic, organic, and biochemical approaches has been developed to study how protein and nucleic acid assemblies modulate the affinity, specificity and cooperativity of protein–nucleic acid interactions. These strategies have enabled formation of noncovalent peptide dimers on specific DNA sequences. A new framework from RNA and peptide into a stable complex of ribonucleopeptide was also developed to construct receptors and fluorescent sensors for small molecules. Attempts to design novel DNA-binding peptides, receptors and sensors will provide an ultimate test for our understanding of the principle of molecular recognition associated with protein–nucleic acid interactions.

Molecular Recognition in the Colloidal World.

Colloidal self-assembly is a bottom-up technique to fabricate functional nanomaterials, with paramount interest stemming from programmable assembly of smaller building blocks into dynamic crystalline domains and photonic materials. Multiple established colloidal platforms feature diverse shapes and bonding interactions, while achieving specific orientations along with short- and long-range order. A major impediment to their universal use as building blocks for predesigned architectures is the inability to precisely dictate and control particle functionalization and concomitant reversible self-assembly. Progress in colloidal self-assembly necessitates the development of strategies that endow bonding specificity and directionality within assemblies. Methodologies that emulate molecular and polymeric three-dimensional (3D) architectures feature elements of covalent bonding, while high-fidelity molecular recognition events have been installed to realize responsive reconfigurable assemblies. The emergence of anisotropic 'colloidal molecules', coupled with the ability to site-specifically decorate particle surfaces with supramolecular recognition motifs, has facilitated the formation of superstructures via directional interactions and shape recognition. In this Account, we describe supramolecular assembly routes to drive colloidal particles into precisely assembled architectures or crystalline lattices via directional noncovalent molecular interactions. The design principles are based upon the fabrication of colloidal particles bearing surface-exposed functional groups that can undergo programmable conjugation to install recognition motifs with high fidelity. Modular and versatile by design, our strategy allows for the introduction and integration of molecular recognition principles into the colloidal world. We define noncovalent molecular interactions as site-specific forces that are predictable (i.e., feature selective and controllable complementary bonding partners) and can engage in tunable high-fidelity interactions. Examples include metal coordination and host-guest interactions as well as hydrogen bonding and DNA hybridization. On the colloidal scale, these interactions can be used to drive the reversible formation of open structures. Key to the design is the ability to covalently conjugate supramolecular motifs onto the particle surface and/or noncovalently associate with small molecules that can mediate and direct assembly. Efforts exploiting the binding strength inherent to DNA hybridization for the preparation of reversible open-packed structures are then detailed. We describe strategies that led to the introduction of dual-responsive DNA-mediated orthogonal assembly as well as colloidal clusters that afford distinct DNA-ligated close-packed lattices. Further focus is placed on two essential and related efforts: the engineering of complex superstructures that undergo phase transitions and colloidal crystals featuring a high density of functional anchors that aid in crystallization. The design principles discussed in this Account highlight the synergy stemming from coupling well-established noncovalent interactions common on the molecular and polymeric length scales with colloidal platforms to engineer reconfigurable functional architectures by design. Directional strategies and methods such as those illustrated herein feature molecular control and dynamic assembly that afford both open-packed 1D and 2D lattices and are amenable to 3D colloidal frameworks. Multiple methods to direct colloidal assembly have been reported, yet few are capable of crystallizing 2D and 3D architectures of interest for optical data storage, electronics, and photonics. Indeed, early implications are that [supra]molecular control over colloidal assembly can fabricate rationally structured designer materials from simple fundamental building blocks.

Ferrichrome Has Found Its Match: Biomimetic Analogues with Diversified Activity Map Discrete Microbial Targets.

Siderophores provide an established platform for studying molecular recognition principles in biological systems. Herein, the preparation of ferrichrome (FC) biomimetic analogues varying in length and polarity of the amino acid chain separating between the tripodal scaffold and the pendent FeIII chelating hydroxamic acid groups was reported. Spectroscopic and potentiometric titrations determined their iron affinity to be within the range of efficient chelators. Microbial growth promotion and iron uptake studies were conducted on E. coli, P. putida and U. maydis. A wide range of siderophore activity was observed in the current series: from a rare case of a species-specific growth promotor in P. putida to an analogue matching FC in cross-phylum activity and uptake pathway. A fluorescent conjugate of the broad-range analogue visualized siderophore destination in bacteria (periplasmic space) vs. fungi (cytosol) mapping new therapeutic targets. Quantum dots (QDs) decorated with the most potent FC analogue provided a tool for immobilization of FC-recognizing bacteria. Bacterial clusters formed around QDs may provide a platform for their selection and concentration.

Hot-spot identification on a broad class of proteins and RNA suggest unifying principles of molecular recognition.

Chemically diverse fragments tend to collectively bind at localized sites on proteins, which is a cornerstone of fragment-based techniques. A central question is how general are these strategies for predicting a wide variety of molecular interactions such as small molecule-protein, protein-protein and protein-nucleic acid for both experimental and computational methods. To address this issue, we recently proposed three governing principles, (1) accurate prediction of fragment-macromolecule binding free energy, (2) accurate prediction of water-macromolecule binding free energy, and (3) locating sites on a macromolecule that have high affinity for a diversity of fragments and low affinity for water. To test the generality of these concepts we used the computational technique of Simulated Annealing of Chemical Potential to design one small fragment to break the RecA-RecA protein-protein interaction and three fragments that inhibit peptide-deformylase via water-mediated multi-body interactions. Experiments confirm the predictions that 6-hydroxydopamine potently inhibits RecA and that PDF inhibition quantitatively tracks the water-mediated binding predictions. Additionally, the principles correctly predict the essential bound waters in HIV Protease, the surprisingly extensive binding site of elastase, the pinpoint location of electron transfer in dihydrofolate reductase, the HIV TAT-TAR protein-RNA interactions, and the MDM2-MDM4 differential binding to p53. The experimental confirmations of highly non-obvious predictions combined with the precise characterization of a broad range of known phenomena lend strong support to the generality of fragment-based methods for characterizing molecular recognition.