Optimizing fragment and scaffold docking by use of molecular interaction fingerprints

Protein-ligand interaction fingerprints have been used to postprocess docking poses of three ligand data sets: a set of 40 low-molecular-weight compounds from the Protein Data Bank, a collection of 40 scaffolds from pharmaceutically relevant protein ligands, and a database of 19 scaffolds extracted from true cdk2 inhibitors seeded in 2230 scaffold decoys. Four popular docking tools (FlexX, Glide, Gold, and Surflex) were used to generate poses for ligands of the three data sets. In all cases, scoring by the similarity of interaction fingerprints to a given reference was statistically superior to conventional scoring functions in posing low-molecular-weight fragments, predicting protein-bound scaffold coordinates according to the known binding mode of related ligands, and screening a scaffold library to enrich a hit list in true cdk2-targeted scaffolds.     

Novel tertiary amine oxide surfaces that resist nonspecific protein adsorption

Novel surfaces derivatized with tertiary amine oxides have been prepared and tested for their ability to resist nonspecific protein adsorption. The oxidation of tertiary amines supported on triazine units was carried out using mCPBA to give a format allowing conjugation of biologically active ligands alongside them. Adsorption to these surfaces was tested and compared to adsorption to a set of commercial and custom oligo-/poly(ethylene glycol) (OEG/PEG) supports by challenging them with a protein display library presented on bacteriophage lambda. The new class of amine oxide surfaces is found to compare favorably with the performance of the OEG/PEG supports in the prevention of nonspecific binding.     

Molecular orientation in helical and all-trans oligo(ethylene glycol)-terminated assemblies on gold: results of ab initio modeling

The structural properties of self-assembled monolayers (SAMs) of oligo(ethylene glycol) (OEG)-terminated and amide-containing alkanethiols (HS(CH(2))(15)CONH(CH(2)CH(2)O)(6)H and related molecules with shorter alkyl or OEG portions) on gold are addressed. Optimized geometry of the molecular constituents, characteristic vibration frequencies, and transition dipole moments are obtained using density-functional theory methods with gradient corrections. These data are used to simulate IR reflection-absorption (RA) spectra associated with different OEG conformations. It is shown that the positions and relative intensities of all characteristic peaks in the fingerprint region are accurately reproduced by the model spectra within a narrow range of the tilt and rotation angles of the alkyl plane, which turns out to be nearly the same for the helical and all-trans OEG conformations. In contrast, the tilt of the OEG axis changes considerably under conformational transition from helical to all-trans OEG. By means of ab initio modeling, we also clarify other details of the molecular structure and orientation, including lateral hydrogen bonding, the latter of which is readily possessed by the SAMs in focus. These results are crucial for understanding phase and folding characteristics of OEG SAMs and other complex molecular assemblies. They are also expected to contribute to an improved understanding of the interaction with water, ions, and ultimately biological macromolecules.     

Protein-resistant self-assembled monolayers on gold with latent aldehyde functions

In the present study, oligo(ethylene glycol) (OEG)-linked alkanethiols were synthesized which carry a vicinal diol on one end of the OEG chain. After self-assembled monolayer (SAM) formation on gold, the vicinal diols were converted into aldehyde functions by exposure to aqueous NaIO4, as previously used for SAMs with OEG chains buried in the center of the SAM [Jang et al. Nano Lett. 2003, 3, 691-694]. Mixed SAMs with latent aldehydes on 5% of the OEG termini showed high protein resistance, which greatly slowed the kinetics of protein coupling on the time scale of minutes. Small bioligands (such as biocytin hydrazide) or small heterobifunctional crosslinkers (maleimidopropionyl hydrazide, pyridyldithiopropionyl hydrazide) with hydrazide functions were efficiently bound to the aldehyde functions on the SAM, providing for specific capture of streptavidin or for fast covalent binding of proteins with free thiols or maleimide functions, respectively. In conclusion, OEG-terminated SAMs with latent aldehydes serve as protein-resistant sensor surfaces which are easily functionalized with small ligands or with heterobifunctional crosslinkers to which the bait molecule is attached in a subsequent step.     

The assembly state between magnetic nanosensors and their targets orchestrates their magnetic relaxation response

The target-induced clustering of magnetic nanoparticles is typically used for the identification of clinically relevant targets and events. A decrease in the water proton transverse NMR relaxation time, or T(2), is observed upon clustering, allowing the sensitive and accurate detection of target molecules. We have discovered a new mechanistically unique nanoparticle-target interaction resulting in a T(2) increase and demonstrate herein that this increase, and its associated r(2) relaxivity decrease, are also observed upon the interaction of the nanoparticles with ligands or molecular entities. Small molecules, proteins, and a 15-bp nucleic acid sequence were chemically conjugated to polyacrylic-acid-coated iron oxide nanoparticles, and all decreased the original nanoparticle r(2) value. Further experiments established that the r(2) decrease was inversely proportional to the number of ligands bound to the nanoparticle and the molecular weight of the bound ligand. Additional experiments revealed that the T(2)-increasing mechanism was kinetically faster than the conventional clustering mechanism. Most importantly, under conditions that result in T(2) increases, as little as 5.3 fmol of Bacillus anthracis plasmid DNA (pX01 and pX02), 8 pmol of the cholera toxin B subunit (Ctb), and even a few cancer cells in blood were detected. Transition from the binding to the clustering mechanism was observed in the carbohydrate-, Ctb-, and DNA-sensing systems, simply by increasing the target concentration significantly above the nanoparticle concentration, or using Ctb in its pentameric form as opposed to its monomer. Collectively, these results demonstrate that the molecular architectures resulting from the interaction between magnetic nanosensors and their targets directly govern water proton NMR relaxation. We attribute the observed T(2) increases to the bound target molecules partially obstructing the diffusion of solvent water molecules through the superparamagnetic iron oxide nanoparticles' outer relaxation spheres. Finally, we anticipate that this novel interaction can be incorporated into new clinical and field detection applications, due to its faster kinetics relative to the conventional nanoparticle-clustering assays.     

Sodium alginate/magnesium oxide nanocomposite scaffolds for bone tissue engineering

A simple 2‐step method, consisting of film casting and polyvinyl alcohol leaching, is proposed to prepare magnesium oxide (MO) nanoparticle‐reinforced sodium alginate scaffolds with right properties for bone tissue engineering. The cytocompatibility of the as‐prepared scaffolds was also evaluated using the 3‐(4,5‐dimethylthiazol‐2‐yl)‐2,5‐diphenyltetrazolium‐bromide yellow tetrazole assay test, wherein chondrocyte cells had been considered as target cells. According to the results, the ensuing sodium alginate nanocomposites, containing 4‐wt% MO nanoparticles, demonstrated the highest physical and mechanical properties after leaching step. The Young modulus of sodium alginate/4‐wt% MO was improved about 44%, in comparison with that of the pure alginate sample. Furthermore, incorporating MO nanoparticles up to 4 wt% controlled the liquid uptake capacity of scaffolds vis‐à‐vis the resultant pure sodium alginate sample. Moreover, with increasing the nanoparticle content, the antibacterial properties of scaffolds enhanced, but their degradation rates under in vitro conditions tapered off. With the introduction of 3‐ and 4‐wt% MO, the average diameter of the bacterial zone of the scaffold samples reduced to less than 10 mm², suggesting an insensitive antimicrobial performance, compared with the pure sodium alginate and the samples with 1‐ and 2‐wt% MO content, which exhibit antimicrobial sensitivity. 3‐(4,5‐Dimethylthiazol‐2‐yl)‐2,5‐diphenyltetrazolium‐bromide assay test also revealed the cultivated chondrocyte cells on the 4‐wt% MO nanoparticle‐reinforced scaffold possessed better interaction as well as appropriate cell attachment and proliferation than the pristine sodium alginate sample.     

Phase equilibrium studies on rod/solvent and rod/coil/solvent systems containing poly(α, L‐glutamate) having oligo(ethylene glycol) side chains

Phase equilibrium studies for semiconcentrated solutions of rodlike poly(γ‐benzyl L ‐glutamate) having oligo(ethylene glycol) as side chains (PBLG‐g‐OEG) have been investigated. The phase‐boundary concentrations in isotropic and anisotropic phases for N,N‐dimethylformamide (DMF) solution of PBLG‐g‐OEG with short side chains (PBLG2‐g‐380) are higher than those for solution of PBLG‐g‐OEG with long side chains (PBLG2‐g‐770). The lattice theory and the scaled particle theory for nematic solution, which don't distinguish the molecular architecture of the rodlike polymer, cannot explain this experimental result. Repulsive interaction between rodlike polymers by means of the attached side chains is proposed for the molecular orientation of PBLG‐g‐OEG in anisotropic state in order to describe the experimental result. Ternary phase diagrams of PBLG‐g‐OEG/poly(ethylene glycol) (PEG)/DMF show that the miscibility of rodlike PBLG‐g‐OEG and coiled PEG is most enhanced in the system of PBLG2‐g‐770, which has longest and largest amount of side chains. This experimental observation is explained by using the calculation based on the lattice theory and the repulsive interaction of side chains proposed above. © 2000 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 38: 1331–1340, 2000     

Fingerprint directed scaffold hopping for identification of CCR2 antagonists

Chemokine receptors have evolved as attractive targets for disease conditions which arise due to immunomodulation involving host-defense mechanisms. CCR2, a chemokine receptor, is targeted for diseases like arthritis, multiple sclerosis, vascular disease, obesity, and type 2 diabetes. This study provides a new strategy of a ligand based technique which exploits fingerprint led fragment features in conjunction with structure-guided design for identifying new scaffolds for CCR2. A fragment based mining (FBM) technique was employed on a chemical database to identify novel scaffold hops. The hits were subjected to 3-point pharmacophore fingerprint procedures with Tanimoto similarity metric to compare pharmacophoric fingerprints. The final 66 hits generated by these exercises were predicted by the validated HQSAR model, and the top predicted were suggested as probable scaffolds for CCR2 antagonism. The identified scaffolds were validated through molecular docking studies. The ligands were docked by providing receptor flexibility in the extra cellular domain (1 and 3), N terminal domain, and in the transmembrane (TM1 & TM7) helix region with IFD approach. Some of the scaffolds showed H-bonding potential which was not explored by the data set molecules. All identified scaffolds highlighted a key hydrogen bonding interaction with Thr292 as supported by mutational studies. The observed pi stacking interaction with Tyr188 in data set molecules was also produced by the new scaffolds. Taking the advantage of receptor flexibility the scaffolds explored the hydrophobic binding cleft between helix 1 and 7 occupied by residues Leu44, Leu45, Leu48 and Ile300, Ile303, Ile304, respectively. Two of the identified molecules have promising outcomes and can be considered as novel scaffolds for CCR2 binding.     

Chronopotentiometry as a Sensitive Interfacial Characterisation Tool for Peptide Aptamer Monolayers

Constant current chronopotentiometry is employed in conjunction with cyclic voltammetry and ac voltammetry to present in‐depth interfacial characterisations of the adsorption behaviour of a peptide affinity probe (Cys‐p53), of a thiolated hepta(ethylene glycol) (t‐OEG) and of mixed monolayers of these at mercury electrodes. The peptide sequence is derived from the interaction site of the protein p53 with the protein Mdm2. The adsorbed Cys‐p53 peptide is catalytically active towards the hydrogen evolution reaction, giving rise to very intense peaks in chronopotentiometry, whereas the oligo(ethylene glycol) is not. This difference enables one to monitor the presence of the peptide within mixed monolayers. It is shown that in the binary layers, the adsorption of t‐OEG is kinetically favoured while Cys‐p53 is thermodynamically more strongly adsorbed.     

Synthesis of Multivalent Carbohydrate‐Centered Glycoclusters as Nanomolar Ligands of the Bacterial Lectin LecA from Pseudomonas aeruginosa

A family of fifteen glycoclusters based on a cyclic oligo‐(1→6)‐β‐D ‐glucosamine core has been designed as potential inhibitors of the bacterial lectin LecA with various valencies (from 2 to 4) and linkers. Evaluation of their binding properties towards LecA has been performed by a combination of hemagglutination inhibition assays (HIA), enzyme‐linked lectin assays (ELLA), and isothermal titration microcalorimetry (ITC). Divalent ligands displayed dissociation constants in the sub‐micromolar range and tetravalent ligands displayed low nanomolar affinities for this lectin. The influence of the linker could also be demonstrated; aromatic moieties are the best scaffolds for binding to the lectin. The affinities observed in vitro were then correlated with molecular models to rationalize the possible binding modes of these glycoclusters with the bacterial lectin.     

Swelling of polyacrylamide gels in aqueous solutions of ethylene glycol oligomers

Addition of a small amount of ethylene glycol oligomers (OEG), with the number of repeat units y = 2–4, in an aqueous solution leads to the contraction of both linear and cross-linked poly(acrylamide-co-acrylic acid) chains. The results present clear evidence for the screening effect of OEG on the ionic groups of the polymer chains. Measurements indicate that the pre-swollen poly (acrylamide-co-acrylic acid) gels immersed in aqueous OEG solutions are at equilibrium. However, as the molecular weight of OEG increases, these gels cannot attain their equilibrium swelling ratio due to the appearance of non-equilibrium structures. The stability of these structures increases as the initial swelling degree of the gels increases.     

A High Dielectric N‐Type Small Molecular Acceptor Containing Oligoethyleneglycol Side‐Chains for Organic Solar Cells

We report a new small molecular acceptor, ITIC‐OEG, which is based on indacenodithieno[3,2‐b]thiophene and 1,1‐(dicyanomethylene)‐3‐ indanone including oligoethyleneglycol (OEG) side‐chains. ITIC‐OEG was found to have higher dielectric constant (ε_r=5.6) than that of a reference molecule of ITIC with normal alkyl substituents (ε_r=3.9). The dielectric constant of medium influences significantly the exciton binding energy and the resulting charge separation and recombination. The optical, electrochemical and morphological properties of ITIC‐OEG and its photovoltaic characteristics were investigated by blending with a semi‐crystalline donor polymer, PPDT2FBT, with comparison to those of ITIC. ITIC‐OEG shows more red‐shifted absorption and stronger crystalline packing than ITIC. However, the lower photovoltaic performance (with 1.58% power conversion efficiency, PCE) was measured for PPDT2FBT:ITIC‐OEG, compared to PPDT2FBT:ITIC (5.52% PCE). The incompatibility between PPDT2FBT and ITIC‐OEG (due to high hydrophilic nature of OEG chains) resulted in poor intermixing with large domain separation over 300 nm, showing inefficient charge separation and significant charge recombination. Therefore, to investigate the effect of dielectric constant of the materials on the charge separation and recombination, the blend morphology of the PPDT2FBT:ITIC‐OEG should be optimized first by improving their miscibility and phase separation.     

Mechanistic Insight into Heptosyltransferase Inhibition by using Kdo Multivalent Glycoclusters

The synthesis of unprecedented multimeric Kdo glycoclusters based on fullerene and calix[4]arene central scaffolds is reported. The compounds were used to study the mechanism and scope of multivalent glycosyltransferase inhibition. Multimeric mannosides based on porphyrin and pillar[5]arenes were also generated in a controlled manner. Twelve glycoclusters and their monomeric ligands were thus assayed against heptosyltransferase WaaC, which is an important bacterial glycosyltransferase that is involved in lipopolysaccharide biosynthesis. It was first found that all the multimers interact solely with the acceptor binding site of the enzyme even when the multimeric ligands mimic the heptose donor. Second, the novel Kdo glycofullerenes displayed very potent inhibition (K_i=0.14 μm for the best inhibitor); an inhibition level rarely observed with glycosyltransferases. Although the observed “multivalent effects” (i.e., the enhancement of affinity of a ligand when presented in a multimeric fashion) were in general modest, a dramatic effect of the central scaffold on the inhibition level was evidenced: the fullerene and the porphyrin scaffolds being by far superior to the calix‐ and pillar‐arenes. We could also show, by dynamic light scattering analysis, that the best inhibitor had the propensity to form aggregates with the heptosyltransferase. This aggregative property may contribute to the global multivalent enzyme inhibition, but probably do not constitute the main origin of inhibition.     

Giving Gold Wings: Ultrabright and Fragmentation Free Mass Spectrometry Reporters for Barcoding,Bioconjugation Monitoring,and Data Storage

The widespread application of laser desorption/ionization mass spectrometry (LDI-MS) highlights the need for a bright and multiplexable labeling platform. While ligand-capped Au nanoparticles (AuNPs) have emerged as a promising LDI-MS contrast agent, the predominant thiol ligands suffer from low ion yields and extensive fragmentation. In this work, we develop a N-heterocyclic carbene (NHC) ligand platform that enhances AuNP LDI-MS performance. NHC scaffolds are tuned to generate barcoded AuNPs which, when benchmarked against thiol-AuNPs, are bright mass tags and form unfragmented ions in high yield. To illustrate the transformative potential of NHC ligands, the mass tags were employed in three orthogonal applications: monitoring a bioconjugation reaction, performing multiplexed imaging, and storing and reading encoded information. These results demonstrate that NHC-nanoparticle systems are an ideal platform for LDI-MS and greatly broaden the scope of nanoparticle contrast agents.     

Molecular simulation of interaction between passivated gold nanoparticles in supercritical CO2

Molecular dynamics simulations have been performed to study the potential of mean force (PMF) between passivated gold nanoparticles (NPs) in supercritical CO(2) (scCO(2)). The nanoparticle model consists of a 140 atom gold nanocore and a surface self-assembled monolayer, in which two kinds of fluorinated alkanethiols were considered. The molecular origin of the thermodynamics interaction and the solvation effect has been comprehensively studied. The simulation results demonstrate that increasing the solvent density and ligand length can enhance the repulsive feature of the free energy between the passivated Au nanoparticles in scCO(2), which is in good agreement with previous experimental results. The interaction forces between the two passivated NPs have been decomposed to reveal various contributions to the free energy. It was revealed that the interaction between capping ligands and the interaction between the capping ligands and scCO(2) solvent molecules cooperatively determine the total PMF. A thermodynamic entropy-energy analysis for each PMF contribution was used to explain the density dependence of PMF in scCO(2) fluid. Our simulation study is expected to provide a novel microscopic understanding of the effect of scCO(2) solvent on the interaction between passivated Au nanoparticles, which is helpful to the dispersion and preparation of functional metal nanoparticles in supercritical fluids.     

Interfacial activity of polymer-coated gold nanoparticles

A systematic study of the interfacial activity of polymer-coated gold nanoparticles was performed with the use of a computer-controlled four-roll mill. The nanoparticle locality within the polymeric domains (bulk or interface) was controlled by means of a mixture of polymeric ligands grafted to the gold nanoparticle core. The bulk polymers were polybutadiene (PBd) and polydimethylsiloxane (PDMS). Monoterminated PDMS and PBd ligands were synthesized on the basis of the esterification of reactive groups (such as hydroxyl or amino groups) with lipoic acid anhydride. The formation of polymer-coated nanoparticles using these lipoic acid-functionalized polymers was confirmed via transmission electron microscopy (TEM), and their interfacial activity was manifested as a reduction of the interfacial tension and in the enhanced stability of thin films (as seen via the inhibition of coalescence). The nanoparticles showed an equal, if not superior, ability to reduce the interfacial tension when compared to previous studies on the effect of insoluble surfactants; however, these particles proved not to be as effective at inhibiting coalescence as their surfactant counterpart. We suggest that this effect may be caused by an increase in the attractive van der Waals forces created by the presence of metal-core nanoparticles. Experimental measurements using the four-roll mill allow us to explore the relationship between nanoparticle concentration at the interface and interfacial tension. In particular, we have found evidence that the interface concentration can be increased relative to the equilibrium value achieved by diffusion alone, and thus the interfacial tension can be systematically reduced if the interfacial area is increased temporarily via drop deformation or breakup followed by recoalescence.     

Synthesis, photoluminescence, and adsorption of CdS/dendrimer nanocomposites

CdS/dendrimer nanocomposites can be synthesized from methanolic Cd(2+) and S(2-) with amine-terminated polyamidoamine dendrimers of generation 8 (G8NH(2)) as stabilizers. By controlling the preparation conditions, nanoparticles with diameters < or = 2 nm can be obtained with a narrow size distribution. They show blue photoluminescence at approximately 450 nm. We studied the effects of various additives on the photoluminescence and elucidated its mechanism. Stable aggregates of two to three G8NH(2) molecules with several CdS nanoparticles form; the particles are located at the surface of the G8NH(2) molecules. The adsorption of the CdS/G8NH(2) nanocomposites on flat substrate surfaces is determined by the substrate chemistry. The hydrophilic nature of G8NH(2) results in weak affinity to graphite but strong affinity to hydroxy-terminated substrates such as mica, oxidized silicon wafers, and carboxylate-terminated monolayers. Patterning of nanocomposites on these hydrophilic substrates is achieved by the microcontact printing method. We propose to use only one molecule, a large dendrimer, to control the nanoparticle formation and also the immobilization of the synthesized nanoparticle/dendrimer composites.     

Promotion of sugar-lectin recognition through the multiple sugar presentation offered by regioselectively addressable functionalized templates (RAFT): a QCM-D and SPR study

The investigation of recognition events between carbohydrates and proteins, especially the understanding of how spatial factors and binding avidity are correlated, remains a great interest for glycobiology. In this context we have investigated by nanogravimetry (QCM-D) and surface plasmon resonance (SPR), the kinetics and thermodynamics of the interaction between concanavalin A (Con A) and various neoglycopeptide ligands of low molecular weight. Regioselectively addressable functionalized templates (RAFT) have been used as scaffolds for the design of multivalent neoglycopeptides bearing thiol or biotin functions for their anchoring on transducer surfaces. Although these multivalent neoglycopeptide ligands cannot span multiple binding sites within the same Con A protein, they have increased activities relative to their monovalent counterpart. Our results emphasize that the multivalent RAFT ligands function by clustering several lectins, which leads to enhanced affinities.     

Ligand Conformation Dictates Membrane and Endosomal Trafficking of Arginine‐Glycine‐Aspartate (RGD)‐Functionalized Mesoporous Silica Nanoparticles

Recent breakthrough research on mesoporous silica nanoparticle (MSN) materials has illustrated their significant potential in biological applications due to their excellent drug delivery and endocytotic behavior. We set out to determine if MSN, covalently functionalized with conformation specific bioactive molecules (either linear or cyclic RGD ligands), behave towards mammalian cells in a similar manner as the free ligands. We discovered that RGD immobilized on the MSN surface did not influence the integrity of the porous matrix and improved the endocytosis efficiency of the MSN materials. Through competition experiments with free RGD ligands, we also discovered a conformation specific receptor–integrin association. The interaction between RGD immobilized on the MSN surface and integrins plays an important role in endosome trafficking, specifically dictating the kinetics of endosomal escape. Thus, covalent functionalization of biomolecules on MSN assists in the design of a system for controlling the interface with cancer cells.     

Ligand conformation dictates membrane and endosomal trafficking of arginine-glycine-aspartate (RGD)-functionalized mesoporous silica nanoparticles

Recent breakthrough research on mesoporous silica nanoparticle (MSN) materials has illustrated their significant potential in biological applications due to their excellent drug delivery and endocytotic behavior. We set out to determine if MSN, covalently functionalized with conformation specific bioactive molecules (either linear or cyclic RGD ligands), behave towards mammalian cells in a similar manner as the free ligands. We discovered that RGD immobilized on the MSN surface did not influence the integrity of the porous matrix and improved the endocytosis efficiency of the MSN materials. Through competition experiments with free RGD ligands, we also discovered a conformation specific receptor-integrin association. The interaction between RGD immobilized on the MSN surface and integrins plays an important role in endosome trafficking, specifically dictating the kinetics of endosomal escape. Thus, covalent functionalization of biomolecules on MSN assists in the design of a system for controlling the interface with cancer cells.