Streptavidin binding bifunctional aptamers and their interaction with low molecular weight ligands

This paper describes the measurement of the binding affinities of two bifunctional RNA aptamers to their respective ligands. The aptamers comprise either a theophylline or malachite green binding sequence fused to a streptavidin binding sequence. These bifunctional aptamers are shown to bind simultaneously to both the small ligand and to streptavidin whether in free solution or on gold surfaces. Binding isotherms for both interactions were measured by different physiochemical techniques: surface plasmon resonance, fluorescence spectroscopy and dynamic light scattering. Both qualitatively and quantitatively there is little difference in binding affinities between the bifunctional aptamers and their monofunctional components. The respective K_d values for streptavidin binding in the monofunctional aptamer and in the theophylline bifunctional aptamer were 12 nM and 65 nM, respectively whilst the K_d values for theophylline binding in the monofunctional aptamer and the streptavidin bifunctional aptamer were 300 nM and 120 nM. These results are consistent with treating each aptamer sequence as a module that can be combined with others without significant loss of function. This allows for the use of streptavidin based immobilization strategies without either the cost of biotinylated dNTPs or the variable yields associated with the chemical biotinylation of RNA.     

Identifying the binding mode of a molecular scaffold

We describe a method for docking of a scaffold-based series and present its advantages over docking of individual ligands, for determining the binding mode of a molecular scaffold in a binding site. The method has been applied to eight different scaffolds of protein kinase inhibitors (PKI). A single analog of each of these eight scaffolds was previously crystallized with different protein kinases. We have used FlexX to dock a set of molecules that share the same scaffold, rather than docking a single molecule. The main mode of binding is determined by the mode of binding of the largest cluster among the docked molecules that share a scaffold. Clustering is based on our 'nearest single neighbor' method [J. Chem. Inf. Comput. Sci., 43 (2003) 208-217]. Additional criteria are applied in those cases in which more than one significant binding mode is found. Using the proposed method, most of the crystallographic binding modes of these scaffolds were reconstructed. Alternative modes, that have not been detected yet by experiments, could also be identified. The method was applied to predict the binding mode of an additional molecular scaffold that was not yet reported and the predicted binding mode has been found to be very similar to experimental results for a closely related scaffold. We suggest that this approach be used as a virtual screening tool for scaffold-based design processes.     

DNA:chitosan complex,known as a drug delivery system,can create a porous scaffold

Supramolecular structure can be formed using noncovalent interactions based on the self-assembly processes. DNA is a good example for supramolecular materials because it is able to form supramolecular structure by forming specific hydrogen bonds between its base pairs. Moreover, DNA as an anionic medium can bind with oppositely charged materials to form complex structures of various shapes and properties. This work is focused on a foam complex that is formed between negatively charged DNA and positive chitosan. Various characterizations —Fourier transformed infrared spectroscopy (FTIR), Small and Wide-angle X-ray scattering (SAXS and WAXS), scanning electron microscope (SEM), texture analyzer and differential scanning calorimetry (DSC) — are used to study the properties of this dried scaffold. The FTIR spectra presented the chemical structure of DNA and chitosan. While the SAXS power law decay has revealed that an increasing of chitosan content smoothens the surface of the structure, on the other hand, the roughness is much higher when the DNA content is increased. The melting point of the foam from the DSC scan has been identified. The mechanical property of foam is suitable for the application of scaffold, and there is no cytotoxicity of foam to the cell. It is expected that this type of biomaterial could be used in several applications such as functional material and as a drug delivery material.     

Computational prediction and biochemical characterization of novel RNA aptamers to Rift Valley fever virus nucleocapsid protein

Rift Valley fever virus (RVFV) is a potent human and livestock pathogen endemic to sub-Saharan Africa and the Arabian Peninsula that has potential to spread to other parts of the world. Although there is no proven effective and safe treatment for RVFV infections, a potential therapeutic target is the virally encoded nucleocapsid protein (N). During the course of infection, N binds to viral RNA, and perturbation of this interaction can inhibit viral replication. To gain insight into how N recognizes viral RNA specifically, we designed an algorithm that uses a distance matrix and multidimensional scaling to compare the predicted secondary structures of known N-binding RNAs, or aptamers, that were isolated and characterized in previous in vitro evolution experiment. These aptamers did not exhibit overt sequence or predicted structure similarity, so we employed bioinformatic methods to propose novel aptamers based on analysis and clustering of secondary structures. We screened and scored the predicted secondary structures of novel randomly generated RNA sequences in silico and selected several of these putative N-binding RNAs whose secondary structures were similar to those of known N-binding RNAs. We found that overall the in silico generated RNA sequences bound well to N in vitro. Furthermore, introduction of these RNAs into cells prior to infection with RVFV inhibited viral replication in cell culture. This proof of concept study demonstrates how the predictive power of bioinformatics and the empirical power of biochemistry can be jointly harnessed to discover, synthesize, and test new RNA sequences that bind tightly to RVFV N protein. The approach would be easily generalizable to other applications.     

Minimum sequence requirements for selective RNA-ligand binding: a molecular mechanics algorithm using molecular dynamics and free-energy techniques

In vitro evolution techniques allow RNA molecules with unique functions to be developed. However, these techniques do not necessarily identify the simplest RNA structures for performing their functions. Determining the simplest RNA that binds to a particular ligand is currently limited to experimental protocols. Here, we introduce a molecular-mechanics based algorithm employing molecular dynamics simulations and free-energy methods to predict the minimum sequence requirements for selective ligand binding to RNA. The algorithm involves iteratively deleting nucleotides from an experimentally determined structure of an RNA-ligand complex, performing energy minimizations and molecular dynamics on each truncated structure, and assessing which truncations do not prohibit RNA binding to the ligand. The algorithm allows prediction of the effects of sequence modifications on RNA structural stability and ligand-binding energy. We have implemented the algorithm in the AMBER suite of programs, but it could be implemented in any molecular mechanics force field parameterized for nucleic acids. Test cases are presented to show the utility and accuracy of the methodology.     

Strategy to design aqueous-soluble iron-oxide molecular cluster and nanostructure using polyoxometalate ligand scaffold

Profound availability of iron on earth crust and diversely accessible redox states, makes it a significant metal ion in biology as well as to design molecular catalysts and nanostructured materials. Low-oxidation potential and prone to hydrolysis in an aqueous medium, predominantly in neutral to basic pH, of the divalent iron in the active site of the catalysts, results in the formation of bulk and/or colloidal ferric-hydroxide, oxy-hydroxide, and -oxide. However, nature has developed its own strategy to preserve iron-oxide cluster core, e.g., Ferritin, without aggregation in physiological pH via designing protein scaffold as protector ligand. Although molecular iron-oxo clusters, isolated by using small organic ligands, are depicted as potent catalysts, they usually don't sustain under catalytic turnover condition. In this context, the isolation of multinuclear iron-oxo clusters soluble in water and their subsequent catalysis in the aqueous phase remains a perdurable challenge. Polyoxometalates (POM) are themselves small metal-oxo cluster anions where the metals are in the highest valent-state and a diverse POM structure can be obtained simply by varying the metal ions. Depending on the structure of the POM, the available terminal or bridging oxo groups can act as donor atoms to one or more iron centers. Consequently, a variety of iron clusters can be stabilized by using POM scaffold. Thereby, polyoxoanions, extremely aqueous-soluble and oxidatively inert under reaction conditions, behaved as versatile ligand platform to stabilize iron clusters of different nuclearity (n = 2–30) in water. Moreover, different possible structures and diversity in chemical property by varying hetero atoms or metal ions led to the isolation of a unique aqueous soluble iron-oxide and/or iron-oxy-hydroxide nanostructure where a significant number of polyoxoanions were covalently attached, making them extremely soluble nanostructures. This review summarizes the adapted synthetic strategies to isolate such molecular and nano-scopic iron clusters stabilized by POM anions and describes their stability in an aqueous medium and showcases their prospective applications in different emerging areas.     

Evaluation of a method for controlling molecular scaffold diversity in de novo ligand design

We describe an algorithm for the automated generation of molecular structures subject to geometric and connectivity constraints. The method relies on simulated annealing and simplex optimization of a penalty function that contains a variety of conditions and can be useful in structure-based drug design projects. The procedure controls the diversity and complexity of the generated molecules. Structure selection filters are an integral part and drive the algorithm. Several procedures have been developed to achieve reliable control. A number of template sets can be defined and combined to control the range of molecules which are searched. Ring systems are predefined. Normally, the ring-system complexity is one of the most elusive and difficult factors to control when fusion-, bridge- and spiro-structures are built by joining templates. Here this is not an issue; the decision about which systems are acceptable, and which are not, is made before the run is initiated. Queries for inclusion and exclusion spheres are incorporated into the objective function, and, by using a flexible notation, the structure generation can be directed and more focused. Simulated annealing is a reliable optimizer and converges asymptotically to the global minimum. The objective functions used here are degenerate, so it is likely that each run will produce a different set of good solutions.     

Click to fit: versatile polyvalent display on a peptidomimetic scaffold

We describe an efficient protocol to effect multisite conjugation reactions to oligomers on solid-phase support. Sequence-specific N-substituted glycine "oligopeptoids" were utilized as substrates for azide-alkyne cycloaddition reactions. Diverse groups, including nucleobases and fluorophores, were conjugated at up to six positions on peptoid side chains with yields ranging from 88 to 96%. This strategy will be broadly applicable for generating polyvalent displays on peptides and other scaffolds, allowing precise control of spacing between the displayed groups.     

A two-step stimulus-response cell-SELEX method to generate a DNA aptamer to recognize inflamed human aortic endothelial cells as a potential in vivo molecular probe for atherosclerosis plaque detection

Aptamers are single-stranded oligonucleotides that are capable of binding wide classes of targets with high affinity and specificity. Their unique three-dimensional structures present numerous possibilities for recognizing virtually any class of target molecules, making them a promising alternative to antibodies used as molecular probes in biomedical analysis and clinical diagnosis. In recent years, cell-systematic evolution of ligands by exponential enrichment (SELEX) has been used extensively to select aptamers for various cell targets. However, aptamers that have evolved from cell-SELEX to distinguish the “stimulus-response cell” have not previously been reported. Moreover, a number of cumbersome and time-consuming steps involved in conventional cell-SELEX reduce the efficiency and efficacy of the aptamer selection. Here, we report a “two-step” methodology of cell-SELEX that successfully selected DNA aptamers specifically against “inflamed” endothelial cells. This has been termed as stimulus-response cell-SELEX (SRC-SELEX). The SRC-SELEX enables the selection of aptamers to distinguish the cells activated by stimulus of healthy cells or cells isolated from diseased tissue. We report a promising aptamer, N55, selected by SRC-SELEX, which can bind specifically to inflamed endothelial cells both in cell culture and atherosclerotic plaque tissue. This aptamer probe was demonstrated as a potential molecular probe for magnetic resonance imaging to target inflamed endothelial cells and atherosclerotic plaque detection.

Force-field development and molecular dynamics simulations of ferrocene-peptide conjugates as a scaffold for hydrogenase mimics

The increasing importance of hydrogenase enzymes in the new energy research field has led us to examine the structure and dynamics of potential hydrogenase mimics, based on a ferrocene-peptide scaffold, using molecular dynamics (MD) simulations. To enable this MD study, a molecular mechanics force field for ferrocene-bearing peptides was developed and implemented in the CHARMM simulation package, thus extending the usefulness of the package into peptide-bioorganometallic chemistry. Using the automated frequency-matching method (AFMM), optimized intramolecular force-field parameters were generated through quantum chemical reference normal modes. The partial charges for ferrocene were derived by fitting point charges to quantum-chemically computed electrostatic potentials. The force field was tested against experimental X-ray crystal structures of dipeptide derivatives of ferrocene-1,1'-dicarboxylic acid. The calculations reproduce accurately the molecular geometries, including the characteristic C2-symmetrical intramolecular hydrogen-bonding pattern, that were stable over 0.1 micros MD simulations. The crystal packing properties of ferrocene-1-(D)alanine-(D)proline-1'-(D)alanine-(D)proline were also accurately reproduced. The lattice parameters of this crystal were conserved during a 0.1 micros MD simulation and match the experimental values almost exactly. Simulations of the peptides in dichloromethane are also in good agreement with experimental NMR and circular dichroism (CD) data in solution. The developed force field was used to perform MD simulations on novel, as yet unsynthesized peptide fragments that surround the active site of [Ni-Fe] hydrogenase. The results of this simulation lead us to propose an improved design for synthetic peptide-based hydrogenase models. The presented MD simulation results of metallocenes thereby provide a convincing validation of our proposal to use ferrocene-peptides as minimal enzyme mimics.     

Nanostaircase formation in the solid state from self-assembling synthetic terephthalamides with a common molecular scaffold

The design and construction of nanostructured materials using proper self-assembling molecular building blocks is a real challenge to scientists. Here, we present the formation of a new nano-architecture, i.e., nanostaircase in the solid state by using molecular building blocks, which are amenable to self-assembly in a directed manner to form the specific nanostructure. The molecular building blocks are terephthalamides 1-4, which are bis-terephthalamides of methyl esters of various α-amino acids including l-leucine 1, d-leucine 2, l-isoleucine 3, and α-aminoisobutyric acid (Aib) 4. All terephthalamides presented here, irrespective of their different side chain residues or stereochemistry, self-assemble to form supramolecular nanostaircase structures in crystals. Each terephthalamide contains two good hydrogen-bond donors and two hydrogen-bond acceptors. Two N-H?O hydrogen bonds and C-H?π interactions are responsible for the formation and stabilization of the nanostaircase structures in crystals. The molecular building blocks are packed orthogonally to each other in crystals and this arrangement can help the formation of nanostaircase structure upon self-assembly.     

A label-free electrochemical biosensor based on a DNA aptamer against codeine

In order to develop a sensor for opium alkaloid codeine detection, DNA aptamers against codeine were generated by SELEX (systematic evolution of ligands by exponential enrichment) technique. An aptamer HL7-14, which is a 37-mer sequence with K_d values of 0.91 μM, was optimized by the truncation-mutation assay. The specificity investigation shows that HL7-14 exhibits high specificity to codeine over morphine, and almost cannot bind to other small molecule. With this new selected aptamer, a novel electrochemical label-free codeine aptamer biosensor based on Au-mesoporous silica nanoparticles (Au-MSN) as immobilized substrate has been proposed using [Fe(CN)₆]^3−/4− as electroactive redox probe. The linear range covered from 10 pM to 100 nM with correlation coefficient of 0.9979 and the detection limit was 3 pM. Our study demonstrates that the biosensor has good specificity, stability and well regeneration. It can be used to detect codeine.     

Combined OX40 Agonist and PD-1 Inhibitor Immunotherapy Improves the Efficacy of Vascular Targeted Photodynamic Therapy in a Urothelial Tumor Model

Purpose: Vascular targeted photodynamic therapy (VTP) is a nonsurgical tumor ablation approach used to treat early-stage prostate cancer and may also be effective for upper tract urothelial cancer (UTUC) based on preclinical data. Toward increasing response rates to VTP, we evaluated its efficacy in combination with concurrent PD-1 inhibitor/OX40 agonist immunotherapy in a urothelial tumor-bearing model. Experimental design: In mice allografted with MB-49 UTUC cells, we compared the effects of combined VTP with PD-1 inhibitor/OX40 agonist with those of the component treatments on tumor growth, survival, lung metastasis, and antitumor immune responses. Results: The combination of VTP with both PD-1 inhibitor and OX40 agonist inhibited tumor growth and prolonged survival to a greater degree than VTP with either immunotherapeutic individually. These effects result from increased tumor infiltration and intratumoral proliferation of cytotoxic and helper T cells, depletion of Treg cells, and suppression of myeloid-derived suppressor cells. Conclusions: Our findings suggest that VTP synergizes with PD-1 blockade and OX40 agonist to promote strong antitumor immune responses, yielding therapeutic efficacy in an animal model of urothelial cancer.     

A molecular model for transcription in the RNA world based on the ribosome large subunit

Examination of the tRNA binding sites in the ribosome suggests that it might once have been able to catalyse the polymerisation of RNA. Based on a viral RNA-dependant RNA polymerase, the geometry of a potential active site for this ribopolymerase was constructed. From examination of the active site geometry, along with other arguments, it is suggested that the ribopolymerase synthesised a parallel complementary strand. When combined into a dimeric polymerase, this strategy minimises the exposure of single-stranded RNA and prevents self-hybridisation: both previously difficult problems for the RNA world hypothesis.     

A diversity-oriented-synthesis protocol for scaffold discovery based on a general synthetic route to spirocycles

A diversity-oriented synthesis (DOS) protocol for scaffold discovery is described. A general synthetic route is developed from a single lactam for the access to various multi-functionalized spirocyclic keto-lactams and their derived spirocyclic keto-amines. This work provides the foundation for a sequential DOS strategy from scaffold discovery to drug discovery.     

G-quartets 40 years later: from 5'-GMP to molecular biology and supramolecular chemistry

Molecular self-assembly is central to many processes in both biology and supramolecular chemistry. The G-quartet, a hydrogen-bonded macrocycle formed by cation-templated assembly of guanosine, was first identified in 1962 as the basis for the aggregation of 5'-guanosine monophosphate. We now know that many nucleosides, oligonucleotides, and synthetic derivatives form a rich array of functional G-quartets. The G-quartet surfaces in areas ranging from structural biology and medicinal chemistry to supramolecular chemistry and nanotechnology. This Review integrates and summarizes knowledge gained from these different areas, with emphasis on G-quartet structure, function, and molecular recognition.     

Synthesis of a β-strand mimetic based on a pyridine scaffold

A synthetic route to a 2,4-disubstituted pyridine as a potential β-strand mimetic has been developed and applied in the synthesis of a tripeptidomimetic of Leu-Gly-Gly. The pyridine scaffold replaces the central glycine, and is substituted with analogues of leucine and glycine in positions 4 and 2, respectively. 2-Fluoro-4-iodopyridine was chosen as the functionalized scaffold and was substituted with protected leucinal in position 4 via a Grignard exchange reaction using iso-propyl magnesium chloride. The glycine moiety was introduced in position 2 via a nucleophilic aromatic substitution reaction (S_NAr) facilitated by microwave irradiation. The synthetic sequence involved 12 steps with an overall yield of 7%.