Small Probe Molecules Research Articles

Conservation of Allosteric Ligand Binding Sites in G-Protein Coupled Receptors.

Despite the growing number of G protein-coupled receptor (GPCR) structures, only 39 structures have been cocrystallized with allosteric inhibitors. These structures have been studied by protein mapping using the FTMap server, which determines the clustering of small organic probe molecules distributed on the protein surface. The method has found druggable sites overlapping with the cocrystallized allosteric ligands in 21 GPCR structures. Mapping of Alphafold2 generated models of these proteins confirms that the same sites can be identified without the presence of bound ligands. We then mapped the 394 GPCR X-ray structures available at the time of the analysis (September 2020). Results show that for each of the 21 structures with bound ligands there exist many other GPCRs that have a strong binding hot spot at the same location, suggesting potential allosteric sites in a large variety of GPCRs. These sites cluster at nine distinct locations, and each can be found in many different proteins. However, ligands binding at the same location generally show little or no similarity, and the amino acid residues interacting with these ligands also differ. Results confirm the possibility of specifically targeting these sites across GPCRs for allosteric modulation and help to identify the most likely binding sites among the limited number of potential locations. The FTMap server is available free of charge for academic and governmental use at https://ftmap.bu.edu/.

An RNA-dependent RNA polymerase inhibitor for tick-borne encephalitis virus

Tick-borne encephalitis virus (TBEV) is a medically important representative of the Flaviviridae family. The TBEV genome encodes a single polyprotein, which is co/post-translationally cleaved into three structural and seven non-structural proteins. Of the non-structural proteins, NS5, contains an RNA-dependent RNA polymerase (RdRp) domain that is highly conserved and is responsible for the genome replication. Screening for potential antivirals was done using a hybrid receptor and ligand-based pharmacophore search likely targeting the RdRp domain. For the identification of pharmacophores, a mixture of small probe molecules and nucleotide triphosphates were used. The ligand/receptor interaction screenings of structures from the ZINC database resulted in five compounds. Zinc 3677 and 7151 exhibited lower cytotoxicity and were tested for their antiviral effect against TBEV in vitro. Zinc 3677 inhibited TBEV at micromolar concentrations. The results indicate that Zinc 3677 represents a good target for structure-activity optimizations leading potentially to a discovery of effective TBEV antivirals.

Self-Assembly of Bispentadecylphenol Substituted Perylenediimide with PS-b-P4VP for Structure–Property Insight into the Core of Core–Shell Micelles

We report the use of a ditopic molecular probe bispentadecylphenol substituted perylenediimide (PBI–PDP) to examine the molecular level self-assembly of polystyrene-b-poly(4-vinylpyridine) (PS-b-P4VP) in tetrahydrofuran (THF). A series of complexes were prepared between PS-b-P4VP copolymers with varying lengths of the 4-vinylpyridine chain and PBI–PDP. Light scattering and NMR spectroscopic studies reveal that the self-assembled structures of the solid complexes are not fully disrupted when the complexes are dissolved in THF. NMR experimental parameters measured for the small probe molecule provide detailed insights into the structure of the assemblies in solution as well as the interaction between the small molecule and the block copolymer. Such insights can have important implications in manipulating the nanostructure of block copolymer micelles to suit various application requirements. The dynamics and distribution of the PBI–PDP molecules within the assemblies in solution show a dependence on the leng...

Controllable Fabrication of Inhomogeneous Microcapsules for Triggered Release by Osmotic Pressure

Inhomogeneous microcapsules that can encapsulate various cargo for controlled release triggered by osmotic shock are designed and reported. The microcapsules are fabricated using a microfluidic approach and the inhomogeneity of shell thickness in the microcapsules can be controlled by tuning the flow rate ratio of the middle phase to the inner phase. This study demonstrates the swelling of these inhomogeneous microcapsules begins at the thinnest part of shell and eventually leads to rupture at the weak spot with a low osmotic pressure. Systematic studies indicate the rupture fraction of these microcapsules increases with increasing inhomogeneity, while the rupture osmotic pressure decreases linearly with increasing inhomogeneity. The inhomogeneous microcapsules are demonstrated to be impermeable to small probe molecules, which enables long-term storage. Thus, these microcapsules can be used for long-term storage of enzymes, which can be controllably released through osmotic shock without impairing their biological activity. The study provides a new approach to design effective carriers to encapsulate biomolecules and release them on-demand upon applying osmotic shock.

Discontinuity in Fast Dynamics at the Glass Transition of ortho-Terphenyl.

The dynamics of the molecular glass former ortho-terphenyl through the glass transition were observed with two-dimensional infrared vibrational spectroscopy measurements of spectral diffusion using the small probe molecule phenylselenocyanate. Although the slow diffusive motions were not visible on the experimental time scale, a picosecond-scale exponential relaxation was observed at temperatures from above to well below the glass transition temperature. The characteristic time scale has a smooth temperature dependence from the liquid into the glass phase, but the range of vibrational frequencies the probe samples displayed a discontinuity at the glass transition temperature. Complementary pump-probe experiments associate the observed motion with density fluctuations. The key features of the dynamics are reproduced with a simple corrugated well potential energy surface model. In addition, the temperature dependence of the homogeneous vibrational dephasing was found to have a T2 functional form, where T is the absolute temperature.

Diffusion of small particles in polymer films.

The motion of small probe molecules in a two-dimensional system containing frozen polymer chains was studied by means of Monte Carlo simulations. The model macromolecules were coarse-grained and restricted to vertices of a triangular lattice. The cooperative motion algorithm was used to generate representative configurations of macromolecular systems of different polymer concentrations. The remaining unoccupied lattice sites of the system were filled with small molecules. The structure of the polymer film, especially near the percolation threshold, was determined. The dynamic lattice liquid algorithm was then employed for studies of the dynamics of small objects in the polymer matrix. The influence of chain length and polymer concentration on the mobility and the character of motion of small molecules were studied. Short- and long-time dynamic behaviors of solvent molecules were also described. Conditions of anomalous diffusions' appearance in such systems are discussed. The influence of the structure of the matrix of obstacles on the molecular transport was discussed.

How do packing defects modify the cooperative motions in supercooled liquids?

We use molecular dynamic simulations to investigate the relation between the presence of packing defects in a glass-former and the spontaneous cooperative motions called dynamic heterogeneity. For that purpose we use a simple diatomic glass-former and add a small number of larger or smaller diatomic probes. The diluted probes modify locally the packing, inducing structural defects in the liquid, while we find that the number of defects is small enough not to disturb the average structure. We find that a small packing modification around a few molecules can deeply influence the dynamics of the whole liquid, when supercooled. When we use small probe molecules, the dynamics accelerates and the dynamic heterogeneity decreases. In contrast, for large probes the dynamics slows down and the dynamic heterogeneity increases. The induced heterogeneities and transport coefficient modification increase when the temperature decreases and disappear around the onset temperature of the cage dynamics.

Non-covalent interactions between poly(N-isopropylacrylamide) and small aromatic probe molecules studied by NMR spectroscopy

One of the most important goals in drug delivery is to carry drug molecules to their target as selectively and efficiently as possible. To accomplish this goal it is crucial to understand the interactions of carriers and their loading. The interactions between a thermoresponsive potential drug carrier polymer, poly(N-isopropylacrylamide) (PNIPA) and small aromatic probe molecules: phenol, dopamine and indole derivatives including tryptophan were studied by using solution-state NMR spectroscopy. These substances represent structural elements often found in pharmaceutically relevant compounds. The indole ring is an important part of biologically active natural products, it can be found in several plants and animals. To investigate the effect of temperature on binding and the significance of coil-to-globule transition, 1H T1 and T2 relaxation times, 1H one- and two-dimensional nuclear Overhauser effect spectroscopy (NOESY) and diffusion ordered spectroscopy (DOSY) measurements were carried out in D2O and organic solvents. In the case of phenol and indole derivatives a strong interaction was observed above the lower critical solution temperature (LCST), for it to be much weaker below. According to relaxation measurements only the aromatic ring of tryptophan is bound to the polymer. No interaction was observed between dopamine and the polymer.

Signal Amplification Techniques By Effective Use of the Interfacial Region for Field Effect Transistor (FET) Based Biosensing

Highly sensitive method is greatly desirable for detecting protein biomarkers, which exist in most cases at very low concentration. Such performance would also be of utmost importance to the development of early detection test. In the past few years, we have demonstrated sensitive diagnosis of emerging protein diseases by using field effect transistor (FET) biosensor. Among the recent proposed biosensor devices, FET can offer a simple operation and applicable integration as well as miniaturization that are useful for large-scale production and low-cost application test. This promising FET biosensor principally detects the charged target molecules that specifically interact with probe molecule onto the FET gate surface within the Debye length. Therefore, we can construct strategy for signal amplification with the approaches from the probe molecules as well as from the charged target molecule. To date, we have successfully achieved several techniques to improve sensing signal for FET biosensor by applying small probe molecules[1-3] and by enhancing net charges of target molecules[4-6]. Application of small probe molecules Utilization of small probe molecule is beneficial to improve sensitivity of FET biosensor due to the molecular interaction taking place closer to the sensing surface, which leads to the increase of detectable region of charged target molecules within the Debye length. We have shown a good sensitivity of FET biosensor modified with antigen-binding fragment (Fab) instead of native antibody for detecting cancer biomarkers[1]. In addition, by taking the advantages of small probes, we succeeded sensitive detection for influenza virus-related protein and amyloid β protein (Aβ) using glycan[2] and Congo red[3], respectively. Enhancement of net charges of target molecules In this approach, the main idea is to intensify the charge of target molecules that cause an increase of charge density on the sensing surface. For the first case, we have designed a unique dual-ligand binding by adding the second ligand (metal ions) into the target of prion proteins, which clearly showed an enhancement of the sensitivity of FET biosensor[4]. Additionally, we performed a potent model of surfactant conjugated with target molecule that is useful for signal amplification using FET biosensor[5]. In both of these two examples, signal amplification was mainly due to additional charge by introducing other ions or molecules. Furthermore, we also established a straightforward strategy to enhance the charge of protein by direct modification of the concerned target molecule with chemical modification[6]. This technique proved a significant enhancement of signal amplification for the FET-based biosensing detection with high sensitivity. As described above, we proposed two strategies in the signal amplification for FET biosensors and demonstrated their usefulness. These strategies would be applicable to the detection of other proteins, with adjustment to a certain degree depending on binding affinity and amino acid residues of proteins.AcknowledgementsThis work is partly supported by the Center of Innovation Program, Building of Consortia for the Development of Human Resources in Science and Technology and Grant-in-Aid for Young Scientists (B) (16K17498), all from the Ministry of Education, Culture, Sports, Science and Technology (MEXT), Japan.References S. Cheng, K. Hotani, S. Hideshima, S. Kuroiwa, T. Nakanishi, M. Hashimoto, Y. Mori, T. Osaka, Materials, 7, 2490–2500 (2014). S. Hideshima, H. Hinou, D. Ebihara, R. Sato, S. Kuroiwa, T. Nakanishi, S. Nishimura, T. Osaka, Analytical Chemistry, 85, 5641–5644 (2013). S. Hideshima, M. Kobayashi, T. Wada, S. Kuroiwa, T. Nakanishi, N. Sawamura, T. Asahi, T. Osaka, Chemical Communication, 50, 3476–3479 (2014). S. Wustoni, S. Hideshima, S. Kuroiwa, T. Nakanishi, M. Hashimoto, Y. Mori, T. Osaka, Biosensors and Bioelectronics, 67, 256-262 (2015). S. Hideshima, K. Fujita, Y. Harada, M. Tsuna, Y. Seto, S. Sekiguchi, S. Kuroiwa, T. Nakanishi T. Osaka, Sensing and Biosensing Research, 7, 90-94 (2016). S. Wustoni, S. Hideshima, S. Kuroiwa, T. Nakanishi, Y. Mori, T. Osaka, Sensors and Actuators B, 230, 374-379 (2016).

Development of a versatile in vitro platform for studying biological systems using micro-3D printing and scanning electrochemical microscopy.

We report a novel strategy for studying a broad range of cellular behaviors in real time by combining two powerful analytical techniques, micro-3D printing and scanning electrochemical microscopy (SECM). This allows one, in microbiological studies, to isolate a known number of cells in a micrometer-sized chamber with a roof and walls that are permeable to small molecules and observe metabolic products. In such studies, the size and spatial organization of a population play a crucial role in cellular group behaviors, such as intercellular interactions and communication. Micro-3D printing, a photolithographic method for constructing cross-linked protein microstructures, permits one to compartmentalize a small population of microbes by forming a porous roof and walls around cells in situ. Since the roof and walls defining the microchamber are porous, any small molecules can freely diffuse from the chamber to be detected and quantified using SECM. The size of the chamber and the roof permeability can be obtained by SECM using a small probe molecule, ferrocenemethanol (FcMeOH). The chamber permeability to FcMeOH can be tuned by varying printing parameters that influence the cross-linking density of the proteinaceous material. These analyses establish a versatile strategy as a sensitive platform to quantitatively monitor small molecules produced by microbes.

Fiber based optofluidic biosensors

Medicinal diagnosis requires the development of innovative devices allowing the detection of small amounts of biological species. Among the large variety of available biosensors, the ones based on fluorescence phenomenon are really promising. Here, we show a prototype of the basic unit of a multi-sensing biosensor combining optics and microfluidics benefits. This unit makes use of two crossed optical fibers: the first fiber is used to carry small probe molecules droplets and excite fluorescence, while the second one is devoted to target molecules droplets transport and fluorescence detection. Within this scheme, the interaction takes place in each fiber node. The main benefits of this detection setup are the absence of fibers functionalization, the use of microliter volumes of target and probe species, their separation before interaction, and a better detection limit compared to cuvettes setups.

Probing differential hydration of poly(vinylpyrrolidone) thin films using tracer mobility: an insight from fluorescence correlation spectroscopy.

Dynamics of small probe molecules have been routinely used to unravel the intrinsic details of charged ion transport in polymer brushes and polyelectrolyte multilayer (PEM) thin films. However, corresponding morphological properties affected with absorption of moisture have been hardly dealt with despite numerous applications of isotropic thin films in material chemistry and medical purposes. We have explored the overall structural changes associated with plasticization of PVP thin films by probing dynamics of small reporter (rhodamine 6G, Rh6G) molecules using fluorescence correlation spectroscopy (FCS). It was observed that under lesser amounts of absorbed moisture, the rigidity of the film matrix was high enough to inhibit appreciable molecular mobility. Nonetheless, with gradual increase in the moisture level within the film, molecular movement became extremely facile, so much so that it almost attained close to a solution like state. Molecular mobility was found to be dependent on both the method of preparation and the thickness of the thin films. The diffusivities mostly followed anomalous subdiffusive behaviors, reminiscent of dynamics of tracers in crowded cellular environments. The mobility was found to be independent of any electrostatic interaction between probe and polymer thin film. Hence, the tracer dynamics was attributed most likely to the viscoelasticity of the thin film matrix.

Field Effect Transistor Biosensor Using Antigen Binding Fragment for Detecting Tumor Marker in Human Serum.

Detection of tumor markers is important for cancer diagnosis. Field-effect transistors (FETs) are a promising method for the label-free detection of trace amounts of biomolecules. However, detection of electrically charged proteins using antibody-immobilized FETs is limited by ionic screening by the large probe molecules adsorbed to the transistor gate surface, reducing sensor responsiveness. Here, we investigated the effect of probe molecule size on the detection of a tumor marker, α-fetoprotein (AFP) using a FET biosensor. We demonstrated that the small receptor antigen binding fragment (Fab), immobilized on a sensing surface as small as 2–3 nm, offers a higher degree of sensitivity and a wider concentration range (100 pg/mL–1 μg/mL) for the FET detection of AFP in buffer solution, compared to the whole antibody. Therefore, the use of a small Fab probe molecule instead of a whole antibody is shown to be effective for improving the sensitivity of AFP detection in FET biosensors. Furthermore, we also demonstrated that a Fab-immobilized FET subjected to a blocking treatment, to avoid non-specific interactions, could sensitively and selectively detect AFP in human serum.

Periodic Hybrid DFT Approach (Including Dispersion) to MgCl2-Supported Ziegler–Natta Catalysts. 2. Model Electron Donor Adsorption on MgCl2 Crystal Surfaces

The adsorption of small probe molecules (H2O, NH3 and EtOH) and the small model silane Me2Si(OMe)2 on (104) and (110) surfaces of α-MgCl2 have been studied using periodic DFT calculations including a classical correction (of the type f(R)/R6) for dispersion. The results reveal that donors strongly stabilize both crystal surfaces relative to the bulk solid. Moreover, coordination of two donor molecules to the four-coordinate exposed Mg atom of MgCl2 (110) causes this surface to become preferred over MgCl2 (104) surface with only a single donor per exposed Mg. However, coverage also plays an important role. The model silane preferentially adsorbs in bidentate mode on MgCl2 (110), provided that coverage is 0.5 or lower; at full coverage, there is not enough space for such an arrangement, and only a monodentate binding mode is obtained. Such coverage effects should be even more pronounced for the bulkier silanes used as external donors in real MgCl2-supported Ziegler–Natta systems, as tailored experiments seem to confirm.

PH-Induced Modulation of One- and Two-Photon Absorption Properties in a Naphthalene-Based Molecular Probe

Presently, there is a great demand for small probe molecules that can be used for two-photon excitation microscopy (TPM)-based monitoring of intracellular and intraorganelle activity and pH. The candidate molecules should ideally possess a large two-photon absorption cross section with optical properties sensitive to pH changes. In the present work, we investigate the potential of a methoxy napthalene (MONAP) derivative for its suitability to serve as a pH sensor using TPM. Using an integrated approach rooted in hybrid quantum mechanics/molecular mechanics, the structures, dynamics, and the one- and two-photon properties of the probe in dimethylformamide solvent are studied. It is found that the protonated form is responsible for the optical property of MONAP at moderately low pH, for which the calculated pH-induced red shift is in good agreement with experiments. A 2-fold increase in the two-photon absorption cross section in the IR region of the spectrum is predicted for the moderately low pH form of the probe, suggesting that this can be a potential probe for pH monitoring of living cells. We also propose some design principles aimed at obtaining control of the absorption spectral range of the probe by structural tuning. Our work indicates that the integrated approach employed is capable of capturing the pH-induced changes in structure and optical properties of organic molecular probes and that such in silico tools can be used to draw structure-property relationships to design novel molecular probes suitable for a specific application.

Analysis of Beta Amyloid Peptides Employing the Small Probe Molecules

We herein describe an analytical method employing a small molecule array for the characterization of similar proteins based on ligand binding. In this study, 2 different beta amyloids (Abeta(1-40) and (1-42)) were selected as the model compounds. Their primary structures are identical except for 2 additional C-terminal amino acids. However, many studies have observed different biological and chemical characteristics of these peptides. Thus, the ability to distinguish these 2 peptides is important in the diagnosis and development of treatments for related disorders such as Alzheimer's disease. However, strong non-specific binding is usually observed, even when specific antibodies for each peptide are employed. In this study, Abeta(1-40) and Abeta(1-42) peptides were immobilized on a typical 96-well microplate. Twenty different small probe molecules (modified amino acids conjugated with FITC) were applied to the peptides acting as the secondary antibodies and labeling compounds. The results show that specific binding patterns occurred according to Abeta type and the analysis of the patterns can be used to distinguish these 2 similar peptides.

Nanoscale mechanism of molecular transport through the nuclear pore complex as studied by scanning electrochemical microscopy.

The nuclear pore complex (NPC) is the proteinaceous nanopore that solely mediates molecular transport across the nuclear envelope between the nucleus and cytoplasm of a eukaryotic cell. Small molecules (<40 kDa) diffuse through the large pore of this multiprotein complex. A passively impermeable macromolecule tagged with a signal peptide is chaperoned through the nanopore by nuclear transport receptors (e.g., importins) owing to their interactions with barrier-forming proteins. Presently, this bimodal transport mechanism is not well understood and is described by controversial models. Herein, we report on a dynamic and spatially resolved mechanism for NPC-mediated molecular transport through nanoscale central and peripheral routes with distinct permeabilities. Specifically, we develop a nanogap-based approach of scanning electrochemical microscopy to precisely measure the extremely high permeability of the nuclear envelope to a small probe molecule, (ferrocenylmethyl)trimethylammonium. Effective medium theories indicate that the passive permeability of 5.9 × 10(-2) cm/s corresponds to the free diffusion of the probe molecule through ~22 nanopores with a radius of 24 nm and a length of 35 nm. Peripheral routes are blocked by wheat germ agglutinin to yield 2-fold lower permeability for 17 nm-radius central routes. This lectin is also used in fluorescence assays to find that importins facilitate the transport of signal-tagged albumin mainly through the 7 nm-thick peripheral route rather than through the sufficiently large central route. We propose that this spatial selectivity is regulated by the conformational changes in barrier-forming proteins that transiently and locally expand the impermeably thin peripheral route while blocking the central route.

Vibrational solvatochromism and electrochromism. II. Multipole analysis

Small infrared probe molecules have been widely used to study local electrostatic environment in solutions and proteins. Using a variety of time- and frequency-resolved vibrational spectroscopic methods, one can accurately measure the solvation-induced vibrational frequency shifts and the timescales and amplitudes of frequency fluctuations of such IR probes. Since the corresponding frequency shifts are directly related to the local electric field and its spatial derivatives of the surrounding solvent molecules or amino acids in proteins, one can extract information on local electric field around an IR probe directly from the vibrational spectroscopic results. Here, we show that, carrying out a multipole analysis of the solvatochromic frequency shift, the solvatochromic dipole contribution to the frequency shift is not always the dominant factor. In the cases of the nitrile-, thiocyanato-, and azido-derivatized molecules, the solvatochromic quadrupole contributions to the corresponding stretch mode frequency shifts are particularly large and often comparable to the solvatochromic dipole contributions. Noting that the higher multipole moment-solvent electric field interactions are short range effects in comparison to the dipole interaction, the H-bonding interaction-induced vibrational frequency shift can be caused by such short-range multipole-field interaction effects. We anticipate that the present multipole analysis method specifically developed to describe the solvatochromic vibrational frequency shifts will be useful to understand the intermolecular interaction-induced vibrational property changes and to find out a relationship between vibrational solvatochromism and electrochromism of IR probes in condensed phases.

Hydrogen Bonding Network Disruption in Mesoporous Catalyst Supports Probed by PFG-NMR Diffusometry and NMR Relaxometry

The pulsed-field gradient (PFG)-NMR technique has been applied to study molecular diffusion of organic liquids within mesoporous materials used in heterogeneous catalysis, in order to assess the effect of chemical functionalities on the effective self-diffusivity of the probe molecule within the pore space. True tortuosity values of the porous matrix can be calculated from the ratio of the unrestricted free self-diffusivity to the self-diffusivity within the pore space only when the small liquid-phase probe molecules do not have any chemical functionality that interacts within the solid phase (e.g., alkanes). The use of molecules with reactive chemical functionalities gives values heavily dependent on the physical and chemical interactions within the porous medium; hence, these values cannot be defined as tortuosity. Polyols showed an interesting behavior of enhanced rate of self-diffusion within the confined pore space, and this is attributed to the ability of the porous medium to disrupt the extensive intermolecular hydrogen bonding network of polyols.

Probing Alignment and Phase Behavior in Intact Wood Cell Walls Using2H NMR Spectroscopy

This study presents the first application of (2)H NMR spectroscopy to quantify lignocellulose matrix orientation, and it demonstrates the ability to separately investigate oriented and unoriented amorphous domains in intact natural plant tissue. Matrix orientation is evaluated using NMR quadrupolar interactions in small deuterated probe molecules absorbed into bulk Liriodendron tulipifera sapwood. Ethylene glycol-d(4) deuterium spectra reveal two distinct amorphous domains, a highly oriented phase in the secondary wall S2 layer and an isotropic domain probably reflecting the compound middle lamella (CML). The oriented and isotropic signal areas exhibit thermally reversible changes, postulated to reflect probe redistribution between the S2 layer and the CML. Preliminary studies on a more powerful wood swelling agent, N,N-dimethylformamide-d(1), are also discussed. This (2)H NMR technique provides a new avenue for analysis and understanding of lignocellulose ultrastructure and promises to create new insights in correlating biomass processing with morphological change.