Interaction Of Small Molecules Research Articles

The protein and transcript profiles of human semen.

The increasing use of "-omics" (genomic, transcriptomic, proteomic, epigenomic, and metabolomic) high-throughput measurement technologies over the past decade is beginning to reveal the complexity of human biology and physiology through the interactions of DNA, RNA, related proteins and small molecules. In reproductive medicine, the majority of this work, has thus far focused on the female factors, e.g., the oocyte, since they provide both the environment and the majority of elements required for embryogenesis. State-of-the-art sequencing and computational analyses have enabled a deeper understanding of the underlying components. Contrary to being simply a silent delivery vehicle to the oocyte of the packaged male DNA, sperm provide both a specific epigenetically marked genome together with a complex population of RNAs and proteins that are crucial for early embryogenesis. In addition to the sperm, seminal fluid appears to serve multiple roles providing a supplementary series of components that allow the sperm to successfully reach and fertilize the oocyte and prepare the female immune system to tolerate the semiallosteric embryo. A global analysis and review of what is presently known regarding the unique role of each component of the male factor and their associated interactions begins to shed light on this emergent field.

Unstructural biology of the Dengue virus proteins.

In this study, we used a wide spectrum of bioinformatics techniques to evaluate the extent of intrinsic disorder in the complete proteomes of genotypes of four human dengue virus (DENV), to analyze the peculiarities of disorder distribution within individual DENV proteins, and to establish potential roles for the structural disorder with respect to their functions. We show that several proteins (ER, E, 1, 2A and 4A) are predicted to be mostly ordered, whereas four proteins (C, 2k, NS3 and NS5) are expected to have high disorder levels. The profiles of disorder propensities are similar across the four genotypes, except for the NS5 protein. Cleavage sites are depleted in polymorphic sites, and have a high propensity for disorder, especially relative to neighboring residues. Disordered regions are highly polymorphic in type 1 DENV but have a relatively low number of polymorphic sites in the type 4 virus. There is a high density of polymorphisms in proteins 2A and 4A, which are depleted in disorder. Thus, a high density of polymorphism is not unique to disordered regions. Analysis of disorder/function association showed that the predominant function of the disordered regions in the DENV proteins is protein-protein interaction and binding of nucleic acids, metals and other small molecules. These regions are also associated with phosphorylation, which may regulate their function.

Emergence of complex chemistry on an organic monolayer.

In many origin-of-life scenarios, inorganic materials, such as FeS or mineral clays, play an important role owing to their ability to concentrate and select small organic molecules on their surface and facilitate their chemical transformations into new molecules. However, considering that life is made up of organic matter, at a certain stage during the evolution the role of the inorganic material must have been taken over by organic molecules. How this exactly happened is unclear, and, indeed, a big gap separates the rudimentary level of organization involving inorganic materials and the complex organization of cells, which are the building blocks of life. Over the past years, we have extensively studied the interaction of small molecules with monolayer-protected gold nanoparticles (Au NPs) for the purpose of developing innovative sensing and catalytic systems. During the course of these studies, we realized that the functional role of this system is very similar to that typically attributed to inorganic surfaces in the early stages of life, with the important being difference that the functional properties (molecular recognition, catalysis, signaling, adaptation) originate entirely from the organic monolayer rather than the inorganic support. This led us to the proposition that this system may serve as a model that illustrates how the important role of inorganic surfaces in dictating chemical processes in the early stages of life may have been taken over by organic matter. Here, we reframe our previously obtained results in the context of the origin-of-life question. The following functional roles of Au NPs will be discussed: the ability to concentrate small molecules and create different local populations, the ability to catalyze the chemical transformation of bound molecules, and, finally, the ability to install rudimentary signaling pathways and display primitive adaptive behavior. In particular, we will show that many of the functional properties of the system originate from two features: the presence of metal ions that are complexed in the organic monolayer and the multivalent nature of the system. Complexed metal ions play an important role in determining the affinity and selectivity of the interaction with small molecules, but serve also as regulatory elements for determining how many molecules are bound simultaneously. Importantly, neighboring metal ion complexes also create catalytic pockets in which two metal ions cooperatively catalyze the cleavage of an RNA-model compound. The multivalent nature of the system permits multiple noncovalent interactions with small molecules that enhances the affinity, but is also at the basis of simple signal transduction pathways and adaptive behavior.

Understanding Small-Molecule Interactions in Metal-Organic Frameworks: Coupling Experiment with Theory.

Metal-organic frameworks (MOFs) have gained much attention as next-generation porous media for various applications, especially gas separation/storage, and catalysis. New MOFs are regularly reported; however, to develop better materials in a timely manner for specific applications, the interactions between guest molecules and the internal surface of the framework must first be understood. A combined experimental and theoretical approach is presented, which proves essential for the elucidation of small-molecule interactions in a model MOF system known as M2 (dobdc) (dobdc(4-) = 2,5-dioxido-1,4-benzenedicarboxylate; M = Mg, Mn, Fe, Co, Ni, Cu, or Zn), a material whose adsorption properties can be readily tuned via chemical substitution. It is additionally shown that the study of extensive families like this one can provide a platform to test the efficacy and accuracy of developing computational methodologies in slightly varying chemical environments, a task that is necessary for their evolution into viable, robust tools for screening large numbers of materials.

Small molecules and Alzheimer's disease: misfolding, metabolism and imaging.

Small molecule interactions with amyloid proteins have had a huge impact in Alzheimer's disease (AD), especially in three specific areas: amyloid folding, metabolism and brain imaging. Amyloid plaque amelioration or prevention have, until recently, driven drug development, and only a few drugs have been advanced for use in AD. Amyloid proteins undergo misfolding and oligomerization via intermediates, eventually forming protease resistant amyloid fibrils. These fibrils accumulate to form the hallmark amyloid plaques and tangles of AD. Amyloid binding compounds can be grouped into three categories, those that: i) prevent or reverse misfolding, ii) halt misfolding or trap intermediates, and iii) accelerate the formation of stable and inert amyloid fibrils. Such compounds include hydralazine, glycosaminoglycans, curcumin, beta sheet breakers, catecholamines, and ATP. The versatility of amyloid binding compounds suggests that the amyloid structure may serve as a scaffold for the future development of sensors to detect such compounds. Metabolic dysfunction is one of the earliest pathological features of AD. In fact, AD is often referred to as type 3 diabetes due to the presence of insulin resistance in the brain. A recent study indicates that altering metabolism improves cognitive function. While metabolic reprogramming is one therapeutic avenue for AD, it is more widely used in some cancer therapies. FDA approved drugs such as metformin, dichloroacetic acid (DCA), and methylene blue can alter metabolism. These drugs can therefore be potentially applied in alleviating metabolic dysfunction in AD. Brain imaging has made enormous strides over the past decade, offering a new window to the mind. Recently, there has been remarkable development of compounds that have the ability to image both types of pathological amyloids: tau and amyloid beta. We have focused on the low cost, simple to use, near infrared fluorescence (NIRF) imaging probes for amyloid beta (Aβ), with specific attention on recent developments to further improve contrast, specificity, and sensitivity. With advances in imaging technologies, such fluorescent imaging probes will open new diagnostic avenues.

Protein homology reveals new targets for bioactive small molecules.

The functional impact of small molecules is increasingly being assessed in different eukaryotic species through large-scale phenotypic screening initiatives. Identifying the targets of these molecules is crucial to mechanistically understand their function and uncover new therapeutically relevant modes of action. However, despite extensive work carried out in model organisms and human, it is still unclear to what extent one can use information obtained in one species to make predictions in other species. Here, for the first time, we explore and validate at a large scale the use of protein homology relationships to predict the targets of small molecules across different species. Our results show that exploiting target homology can significantly improve the predictions, especially for molecules experimentally tested in other species. Interestingly, when considering separately orthology and paralogy relationships, we observe that mapping small molecule interactions among orthologs improves prediction accuracy, while including paralogs does not improve and even sometimes worsens the prediction accuracy. Overall, our results provide a novel approach to integrate chemical screening results across multiple species and highlight the promises and remaining challenges of using protein homology for small molecule target identification. Homology-based predictions can be tested on our website http://www.swisstargetprediction.ch. david.gfeller@unil.ch or vincent.zoete@isb-sib.ch. Supplementary data are available at Bioinformatics online.

Some like it Hot: Quantification of Biomolecular Interactions using MicroScale Thermophoresis

Characterization of biomolecular interactions, such as protein-protein, protein-nucleic acid or protein-small molecule, provides critical insights into cellular processes, and is essential for the development of drug diagnostics and therapeutics.Here we present a novel, label-free and tether-free technology to analyze picomolar to millimolar affinities of biomolecular interactions by MicroScale Thermophoresis (MST). The entropy of the hydration shell surrounding molecules determines thermophoretic movement. MST exploits this principle by measuring interactions using optically generated temperature gradients. MST detects changes in the size, charge and hydration shell of molecules and measures biomolecule interactions under close-to-native conditions: immobilization-free and in bioliquids of choice, including cell lysates, blood, and serum. Thus, MST measures interactions under close-to-native conditions, and without laborious sample purification. Here, we demonstrate how MST determines the picomolar to millimolar affinities of various protein:protein and protein:small molecule interactions. MST assays are highly adaptable to fit to the diverse requirements of different and complex biomolecules. NanoTemper´s unique technology is ideal for studies requiring flexibility and sensitivity at the experimental scale, making MST suitable for basic research investigations and pharmaceutical applications.

ChemInform Abstract: Modulating Protein—Protein Interactions: The Potential of Peptides

AbstractReview: 156 refs.

Discrimination of "specific" and "nonspecific" binding in two-dimensional photonic crystals.

In this paper, we propose a design for a 2D slab photonic crystal (PhC) virus sensor and an associated signal analysis methodology that together enable single-virus detection while rejecting false positives that occur due to non-specific interactions of serum proteins and small molecules with the sensor surface. The slab-PhC design takes advantage of both the optical and geometrical properties of its incorporated structures by physically limiting virus infiltration to only the most sensitive region of the PhC sensor, while allowing simultaneous measurement of both site-selective virus infiltration and non-specific small molecule accumulation across the device. Notably, the proposed sensor transducer is compatible with both standard semiconductor fabrication procedures and lab-on-a-chip style microfluidic delivery systems. 3D finite-difference time-domain electromagnetic field computation results are presented, the outcomes of which indicate that both specific (target) virus capture and non-specific (non-target) binding can be simultaneously measured and discerned from one another. This type of capacity for background-corrected, single-pathogen target detection would provide a new and novel advancement toward sensitive, label-free virus diagnostics.

Tethering in RNA: an RNA-binding fragment discovery tool.

Tethering has been extensively used to study small molecule interactions with proteins through reversible disulfide bond forming reactions to cysteine residues. We describe the adaptation of Tethering to the study of small molecule binding to RNA using a thiol-containing adenosine analog (ASH). Among 30 disulfide-containing small molecules screened for efficient Tethering to ASH-bearing RNAs derived from pre-miR21, a benzotriazole-containing compound showed prominent adduct formation and selectivity for one of the RNAs tested. The results of this screen demonstrate the viability of using thiol-modified nucleic acids to discover molecules with binding affinity and specificity for the purpose of therapeutic compound lead discovery.

Preparation of ready-to-use small unilamellar phospholipid vesicles by ultrasonication with a beaker resonator

Lipid vesicles are widely used as models to investigate the interactions of proteins, peptides, and small molecules with lipid bilayers. We present a sonication procedure for the preparation of well-defined and ready-to-use small unilamellar vesicles composed of phospholipids with the aid of a beaker resonator. This indirect but efficient sonication method does not require subsequent centrifugation or other purification steps, which distinguishes it from established sonication procedures. Vesicles produced by this method reveal a unimodal size distribution and are unilamellar, as demonstrated by dynamic light scattering and 31P nuclear magnetic resonance spectroscopy, respectively.

Au nanostructured surfaces for electrochemical and localized surface plasmon resonance-based monitoring of α-synuclein-small molecule interactions.

In this proof-of-concept study, the fabrication of novel Au nanostructured indium tin oxide (Au-ITO) surfaces is described for the development of a dual-detection platform with electrochemical and localized surface plasmon resonance (LSPR)-based biosensing capabilities. Nanosphere lithography (NSL) was applied to fabricate Au-ITO surfaces. Oligomers of α-synuclein (αS) were covalently immobilized to determine the electrochemical and LSPR characteristics of the protein. Cyclic voltammetry (CV) and differential pulse voltammetry (DPV) were performed using the redox probe [Fe(CN)6](3-/4-) to detect the binding of Cu(II) ions and (-)-epigallocatechin-3-gallate (EGCG) to αS on the Au-ITO surface. Electrochemical and LSPR data were complemented by Thioflavin-T (ThT) fluorescence, surface plasmon resonance imaging (SPRi), and transmission electron microscopy (TEM) studies. EGCG was shown to induce the formation of amorphous aggregates that decreased the electrochemical signals. However, the binding of EGCG with αS increased the LSPR absorption band with a bathochromic shift of 10-15 nm. The binding of Cu(II) to αS enhanced the DPV peak current intensity. NSL fabricated Au-ITO surfaces provide a promising dual-detection platform to monitor the interaction of small molecules with proteins using electrochemistry and LSPR.

Interaction of ions, atoms, and small molecules with quantized vortex lines in superfluid (4)He.

The interaction of a number of impurities (H2, Ag, Cu, Ag2, Cu2, Li, He3 (+), He(*) ((3)S), He2 (∗) ((3)Σu), and e(-)) with quantized rectilinear vortex lines in superfluid (4)He is calculated by using the Orsay-Trento density functional theory (DFT) method at 0 K. The Donnelly-Parks (DP) potential function binding ions to the vortex is combined with DFT data, yielding the impurity radius as well as the vortex line core parameter. The vortex core parameter at 0 K (0.74 Å) obtained either directly from the vortex line geometry or through the DP potential fitting is smaller than previously suggested but is compatible with the value obtained from re-analysis of the Rayfield-Reif experiment. All of the impurities have significantly higher binding energies to vortex lines below 1 K than the available thermal energy, where the thermally assisted escape process becomes exponentially negligible. Even at higher temperatures 1.5-2.0 K, the trapping times for larger metal clusters are sufficiently long that the previously observed metal nanowire assembly in superfluid helium can take place at vortex lines. The binding energy of the electron bubble is predicted to decrease as a function of both temperature and pressure, which allows adjusting the trap depth for either permanent trapping or to allow thermally assisted escape. Finally, a new scheme for determining the trapping of impurities on vortex lines by optical absorption spectroscopy is outlined and demonstrated for He(*).

Fabrication of planar colloidal clusters with template-assisted interfacial assembly.

The synthesis of nanoparticle clusters, also referred to as colloidal clusters or colloidal molecules, is being studied intensively as a model system for small molecule interactions as well as for the directed self-assembly of advanced materials. This paper describes a technique for the interfacial assembly of planar colloidal clusters using a combination of top-down lithographic surface modification and bottom-up Langmuir-Blodgett deposition. Micrometer sized polystyrene latex particles were deposited onto a chemically modified substrate from a decane-water interface with Langmuir-Blodgett deposition. The surface of the substrate contained hydrophilic domains of various size, spacing, and shape, while the remainder of the substrate was hydrophobic. Particles selectively deposited onto hydrophilic regions from the decane-water interface. The number of deposited particles depended on the size of each patch, thereby demonstrating that tuning cluster size is possible by engineering patch geometry. Following deposition, the clusters were permanently bonded with temperature annealing and then removed from the substrate via sonication. The permanently bonded planar colloidal clusters were stable in an aqueous environment and at a decane-water interface laden with isotropic colloidal particles. The method is a simple and fast way to synthesize colloidal clusters with few limitations on particle chemistry, composition, and shape.

ADME SARfari: comparative genomics of drug metabolizing systems.

Motivation: ADME SARfari is a freely available web resource that enables comparative analyses of drug-disposition genes. It does so by integrating a number of publicly available data sources, which have subsequently been used to build data mining services, predictive tools and visualizations for drug metabolism researchers. The data include the interactions of small molecules with ADME (absorption, distribution, metabolism and excretion) proteins responsible for the metabolism and transport of molecules; available pharmacokinetic (PK) data; protein sequences of ADME-related molecular targets for pre-clinical model species and human; alignments of the orthologues including information on known SNPs (Single Nucleotide Polymorphism) and information on the tissue distribution of these proteins. In addition, in silico models have been developed, which enable users to predict which ADME relevant protein targets a novel compound is likely to interact with.Availability and implementation: https://www.ebi.ac.uk/chembl/admesarfariContact: jpo@ebi.ac.ukSupplementary information: Supplementary data are available at Bioinformatics online.

Nav1.7 Inhibitor, PF-05089771, Inhibits Fast- and Slow-Inactivated Channels with Similar Affinities

Voltage-gated sodium channel (Nav) inhibitors are used clinically as analgesics and local anesthetics. However, the absence of Nav channel isoform selectivity of current treatment options can result in adverse cardiac and CNS side effects, limiting their therapeutic utility. Human hereditary gain- or loss-of-pain disorders have demonstrated an essential role of Nav1.7 sodium channels in the sensation of pain, thus making this channel an attractive target for new pain therapies. We have identified a novel, human Nav1.7 selective inhibitor (PF-05089771, IC50 = 11 nM) that preferentially interacts with, and stabilizes, inactivated conformation(s) of the channel via an interaction with the voltage-sensor domain (VSD) of Domain 4. The current study demonstrates that PF-05089771 exhibits concentration-dependent slowly developing inhibition (tau = 209 sec and 33 sec, at 100 nM and 1 μM, respectively), and a similarly slow recovery from block upon washout (tau ∼7 min). PF-05089771 exhibits minimal use-dependent inhibition until concentrations exceed 10-fold the IC50, which is consistent with the observed slow onset of block and/or a low affinity for resting or fast-inactivated channel conformations. To evaluate this further, we employed whole cell patch clamp protocols to separate channels into predominantly fast- or slow-inactivated Nav populations. Inhibition by PF-05089771 develops with similar rates using protocols that biases for either fast- or slow-inactivated states, suggesting that preference for a particular inactivated state (fast, intermediate or slow) appears less critical than the relative time that the channel is in an inactivated state during compound exposure. The inhibition profile of PF-05089771 suggests that a conformational change in the Domain 4 VSD couples to multiple downstream inactivated states and immobilizing the voltage-sensor via a small molecule interaction with this site may lock the channel into long term inactivation from which recovery is slow.

Platinum and platinum based nanoalloys synthesized by wet chemistry.

Platinum nanocrystals and their derivatives with palladium and cobalt are of fundamental interest due to their wide field of application in chemistry and physics. Their properties are strongly dependent on their shape and composition. However the chemical route is far from allowing control of both shape and composition. In this paper, we show both experimentally and theoretically the important role of the interaction of small adsorbed molecules on the shape but also on the composition. This has been studied by comparing the case of pure palladium and platinum nanocrystals and the case of PtPd and PtCo nanoalloys synthesized by the liquid-liquid phase transfer method.

Enzyme transformation to modulate the ligand-receptor interactions between small molecules.

Enzymatic transformation is a fundamental process to control ligand-receptor interactions among proteins for signal transduction in cells. Here we report the first example of enzymatic transformation regulated ligand-receptor interactions of small molecules, in which enzymatic reaction changes the stoichiometry of the ligand-receptor binding from 1 : 1 to 1 : 2. We also show that this unique integration of enzymatic transformation and ligand-receptor interactions of small molecules is able to affect the fate of cells.

Affinity imaging mass spectrometry (AIMS): high-throughput screening for specific small molecule interactions with frozen tissue sections.

A novel screening system, using affinity imaging mass spectrometry (AIMS), has been developed to identify protein aggregates or organ structures in unfixed human tissue. Frozen tissue sections are positioned on small (millimetre-scale) stainless steel chips and incubated with an extensive library of small molecules. Candidate molecules showing specific affinity for the tissue section are identified by imaging mass spectrometry (IMS). As an example application, we screened over a thousand compounds against Alzheimer's disease (AD) brain tissue and identified several compounds with high affinity for AD brain sections containing tau deposits compared to age-matched controls. It should also be possible to use AIMS to isolate chemical compounds with affinity for tissue structures or components that have been extensively modified by events such as oxidation, phosphorylation, acetylation, aggregation, racemization or truncation, for example, due to aging. It may also be applicable to biomarker screening programs.

Interaction of the Intrinsically Disordered c-Myc Oncoprotein with Racemic and Enantiopure Small Molecules

The prevalence of intrinsically disordered proteins (IDPs) in cell signaling and disease makes them significant targets. Despite the absence of defined tertiary structure, small molecules can bind IDPs at sites determined by a short, linear segment of the protein's primary sequence. The oncoprotein c-Myc, a transcription factor that must undergo coupled folding and binding to its obligate partner Max in order to interact with DNA, is an ideal system for understanding specificity in small-molecule binding to IDPs. Three small molecule interaction sites exist in the bHLHZip region of c-Myc, the segment necessary for coupled folding and binding to Max. The chiral small molecule 10074-A4 interacts with one of these sites (Myc372-389). The presence of Myc372-389 induces small molecule circular dichroism of racemic 10074-A4, indicating an enantiospecific interaction. We have synthesized the pure R and S enantiomers of 10074-A4 (as well as pure enantiomers of derivatives) and found that at 10 uM and above the compound can undergo a transition upon addition to water from an aggregate, to a dispersed molecule, to an assembled chiral complex with a strong CD signature. SPR measurements indicate interaction between Myc and 10074-A4. These data suggest multiple possible binding modes. We also report the hydrodynamic radius of the bHLHZip region of c-Myc, as determined by fluorescence correlation spectroscopy and dynamic light scattering, under different conditions including in the presence of various small molecules and c-Myc's obligate partner Max.