Cyclometalated Gold(III)‐Hydride Complexes Exhibit Visible Light‐Induced Thiol Reactivity and Act as Potent Photo‐Activated Anti‐Cancer Agents

The specific gold‐sulfur binding interaction renders gold complexes as promising anti‐cancer agents that can potentially overcome cisplatin resistance; while their unbiased binding towards non‐tumoral off‐target thiol‐proteins has posed a big hurdle to clinical application. Herein we report that cyclometalated gold(III) complexes bearing hydride ligands are highly stable towards thiols in the dark but can efficiently dissociate the auxiliary hydride moiety and generate a gold‐thiol adduct when excited with visible light. In consequence, the photo‐activated gold(III) complexes potently inhibited thioredoxin reductase in association with up to >400‐fold increment of photocytotoxicity (vs. dark condition) without deactivation by serum albumin and along with strong anti‐angiogenesis activity in zebrafish embryos. Importantly, the gold(III)‐hydride complexes could be activated by two‐photon laser irradiation at the phototherapeutic window as effectively as blue‐light irradiation.     

Substantial Influence of Temperature on Anchoring of Gold‐Nanoparticle Monolayer for Performance of DNA Biosensors

This paper presents a way of modification of crystalline gold surface with a high quality layer of gold nanoparticles (Au NPs) via self‐assembled dithiol. The application of additional Au NPs monolayer prepared at various temperatures was tested with three types of biosensors previously described in the literature. The examined DNA biosensors differed by the detection method and the way of the immobilization of DNA probe at the modified gold electrode surface. For the immobilization of DNA probe in the sensing layer either the formation of SAM or the affinity binding (biotin – sterptavidin) or covalent attachment were used. The necessary condition of successful preparation of a perfect such monolayer is the preparation temperature of 4 °C. The preparation of Au NPs layers at higher than 4 °C temperatures leads to poor repeatability and unsatisfactory precision of the measurements. The application of the perfect Au monolayer lowers the detection limit (circa by 10 to 100 times) for all tested DNA biosensors.     

Substrate‐induced formation of a recognition structure in a four‐polypeptide–lipid monolayer system

Poly(γ‐methyl L ‐glutamate)s with Ser, His, Asp, and Glu residues at the amino terminal as the serine protease catalytic site were prepared. The number‐average degree of polymerization of the polypeptides was 51. A dipalmitoylphosphatidylcholine monolayer containing the polypeptides was formed at the air–water interface and was transferred onto gold‐deposited glass plates. The binding of N‐acetyltyrosine ethyl ester, a typical substrate of the serine protease, to the monolayer was characterized by surface plasmon resonance measurements. The four‐polypeptide–lipid monolayer system conditioned on an aqueous solution containing the substrate N‐acetyltyrosine ethyl ester exhibited Langmuir‐type binding of the substrate. Its binding constant of 6.1 × 10⁴ M⁻¹ was about 20 times larger than that observed for a monolayer prepared on pure water. The behavior may have arisen from a substrate‐induced rearrangement of the four kinds of polypeptides in the monolayer, forming a substrate‐binding structure similar to that found in serine protease. © 2000 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 38: 2186–2191, 2000     

Discovery of Small‐Molecule Interleukin‐2 Inhibitors from a DNA‐Encoded Chemical Library

Libraries of chemical compounds individually coupled to encoding DNA tags (DNA‐encoded chemical libraries) hold promise to facilitate exceptionally efficient ligand discovery. We constructed a high‐quality DNA‐encoded chemical library comprising 30 000 drug‐like compounds; this was screened in 170 different affinity capture experiments. High‐throughput sequencing allowed the evaluation of 120 million DNA codes for a systematic analysis of selection strategies and statistically robust identification of binding molecules. Selections performed against the tumor‐associated antigen carbonic anhydrase IX (CA IX) and the pro‐inflammatory cytokine interleukin‐2 (IL‐2) yielded potent inhibitors with exquisite target specificity. The binding mode of the revealed pharmacophore against IL‐2 was confirmed by molecular docking. Our findings suggest that DNA‐encoded chemical libraries allow the facile identification of drug‐like ligands principally to any protein of choice, including molecules capable of disrupting high‐affinity protein–protein interactions.     

Fast and accurate predictions of binding free energies using MM‐PBSA and MM‐GBSA

In the drug discovery process, accurate methods of computing the affinity of small molecules with a biological target are strongly needed. This is particularly true for molecular docking and virtual screening methods, which use approximated scoring functions and struggle in estimating binding energies in correlation with experimental values. Among the various methods, MM‐PBSA and MM‐GBSA are emerging as useful and effective approaches. Although these methods are typically applied to large collections of equilibrated structures of protein‐ligand complexes sampled during molecular dynamics in water, the possibility to reliably estimate ligand affinity using a single energy‐minimized structure and implicit solvation models has not been explored in sufficient detail. Herein, we thoroughly investigate this hypothesis by comparing different methods for the generation of protein‐ligand complexes and diverse methods for free energy prediction for their ability to correlate with experimental values. The methods were tested on a series of structurally diverse inhibitors of Plasmodium falciparum DHFR with known binding mode and measured affinities. The results showed that correlations between MM‐PBSA or MM‐GBSA binding free energies with experimental affinities were in most cases excellent. Importantly, we found that correlations obtained with the use of a single protein‐ligand minimized structure and with implicit solvation models were similar to those obtained after averaging over multiple MD snapshots with explicit water molecules, with consequent save of computing time without loss of accuracy. When applied to a virtual screening experiment, such an approach proved to discriminate between true binders and decoy molecules and yielded significantly better enrichment curves. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

Multivalent Gold Glycoclusters: High Affinity Molecular Recognition by Bacterial Lectin PA‐IL

Multivalent protein‐carbohydrate interactions are involved in the initial stages of many fundamental biological and pathological processes through lectin–carbohydrate binding. The design of high affinity ligands is therefore necessary to study, inhibit and control the processes governed through carbohydrate recognition by their lectin receptors. Carbohydrate‐functionalised gold nanoclusters (glyconanoparticles, GNPs) show promising potential as multivalent tools for studies in fundamental glycobiology research as well as biomedical applications. Here we present the synthesis and characterisation of galactose functionalised GNPs and their effectiveness as binding partners for PA‐IL lectin from Pseudomonas aeruginosa. Interactions were evaluated by hemagglutination inhibition (HIA), surface plasmon resonance (SPR) and isothermal titration calorimetry (ITC) assays. Results show that the gold nanoparticle platform displays a significant cluster glycoside effect for presenting carbohydrate ligands with almost a 3000‐fold increase in binding compared with a monovalent reference probe in free solution. The most effective GNP exhibited a dissociation constant (K_d) of 50 nM per monosaccharide, the most effective ligand of PA‐IL measured to date; another demonstration of the potential of glyco‐nanotechnology towards multivalent tools and potent anti‐adhesives for the prevention of pathogen invasion. The influence of ligand presentation density on their recognition by protein receptors is also demonstrated.     

Controlled Release of a Sparingly Water‐Soluble Anticancer Drug through pH‐Responsive Functionalized Gold‐Nanoparticle‐Decorated Liposomes

The binding and detachment of carboxyl‐modified gold nanoparticles from liposomes is used for controlled drug delivery. This study reveals that the binding and detachment of nanoparticles from liposomes depends on the degree of hydration of the liposomes. Liposomes with a lower hydration level undergo stronger electrostatic interactions with negatively charged gold nanoparticles, thus leading to a slower detachment of the carboxyl‐modified gold nanoparticles under gastric conditions. Therefore, under gastric conditions, gold‐nanoparticle‐decorated dipalmitoylphosphatidylcholine (DPPC) liposomes exhibit an at least ten‐times‐slower drug release compared to gold‐nanoparticle‐decorated 1,2‐dimyristoyl‐sn‐glycero‐3‐phosphocholine (DMPC) liposomes, although both liposomes in the bare state fail to pursue controlled release. Our study also reveals that one can modulate the drug‐release rate by simply varying the concentration of nanoparticles. This study highlights a novel strategy for the controlled release of drug molecules from liposomes.     

On the Size Evolution of Monolayer‐Protected Gold Clusters during Ligand Place‐Exchange Reactions: The Effect of Solvents

Ligand place‐exchange (LPE) reactions are extensively applied for the post‐functionalization of monolayer‐protected gold clusters (MPCs) by using excessive incoming ligands to displace initial ones. However, the modified MPCs are often enlarged or degraded; this results in ill‐defined size‐dependent properties. The growth of MPCs essentially involves an unprotected surface that is subsequently has gold atoms added or is fused with other gold cores owing to collision. Reported herein is a guideline for the selection of solvents to suppress unwanted MPC growth. Favorable solvents are those with significant affinity to gold or with low solubility for desorbed ligands because these properties retard LPE reactions and minimize the time available for unprotected gold cores. This finding provides a general and convenient approach to regulate the size of functionalized MPCs.     

Effect of Head‐Group Chemistry on Surface‐Mediated Molecular Self‐Assembly

Surface molecular self‐assembly is a fast advancing field with broad applications in sensing, patterning, device assembly, and biochemical applications. A vast number of practical systems utilize alkane thiols supported on gold surfaces. Whereas a strong Au? S bond facilitates robust self‐assembly, the interaction is so strong that the surface is reconstructed, leaving etch pits that render the monolayers susceptible to degradation. By using different head group elements to adcust the molecule–surface interaction, a vast array of new systems with novel properties may be formed. In this paper we use a carefully chosen set of molecules to make a direct comparison of the self‐assembly of thioether, selenoether, and phosphine species on Au(111). Using the herringbone reconstruction of gold as a sensitive readout of molecule–surface interaction strength, we correlate head‐group chemistry with monolayer (ML) properties. It is demonstrated that the hard/soft rules of inorganic chemistry can be used to rationalize the observed trend of molecular interaction strengths with the soft gold surface, that is, P>Se>S. We find that the structure of the monolayers can be explained by the geometry of the molecules in terms of dipolar, quadrupolar, or van der Waals interactions between neighboring species driving the assembly of distinct ordered arrays. As this study directly compares one element with another in simple systems, it may serve as a guide for the design of self‐assembled monolayers with novel structures and properties.     

Free‐Standing Gold‐Nanoparticle Monolayer Film Fabricated by Protein Self‐Assembly of α‐Synuclein

Free‐standing nanoparticle films are of great importance for developing future nano‐electronic devices. We introduce a protein‐based fabrication strategy of free‐standing nanoparticle monolayer films. α‐Synuclein, an amyloidogenic protein, was utilized to yield a tightly packed gold‐nanoparticle monolayer film interconnected by protein β‐sheet interactions. Owing to the stable protein–protein interaction, the film was successfully expanded to a 4‐inch diameter sheet, which has not been achieved with any other free‐standing nanoparticle monolayers. The film was flexible in solution, so it formed a conformal contact, surrounding even microspheres. Additionally, the monolayer film was readily patterned at micrometer‐scale and thus unprecedented double‐component nanoparticle films were fabricated. Therefore, the free‐floating gold‐nanoparticle monolayer sheets with these properties could make the film useful for the development of bio‐integrated nano‐devices and high‐performance sensors.     

Binding structures of tri‐N‐acetyl‐β‐glucosamine in hen egg white lysozyme using molecular dynamics with a polarizable force field

Lysozyme is a well‐studied enzyme that hydrolyzes the β‐(1,4)‐glycosidic linkage of N‐acetyl‐β‐glucosamine (NAG)_n oligomers. The active site of hen egg‐white lysozyme (HEWL) is believed to consist of six subsites, A‐F that can accommodate six sugar residues. We present studies exploring the use of polarizable force fields in conjunction with all‐atom molecular dynamics (MD) simulations to analyze binding structures of complexes of lysozyme and NAG trisaccharide, (NAG)₃. MD trajectories are applied to analyze structures and conformation of the complex as well as protein–ligand interactions, including the hydrogen‐bonding network in the binding pocket. Two binding modes (ABC and BCD) of (NAG)₃ are investigated independently based on a fixed‐charge model and a polarizable model. We also apply molecular mechanics with generalized born and surface area (MM‐GBSA) methods based on MD using both nonpolarizable and polarizable force fields to compute binding free energies. We also study the correlation between root‐mean‐squared deviation and binding free energies of the wildtype and W62Y mutant; we find that for this prototypical system, approaches using the MD trajectories coupled with implicit solvent models are equivalent for polarizable and fixed‐charge models. © 2012 Wiley Periodicals, Inc.     

Multimerization of an Apoptogenic TRAIL‐Mimicking Peptide by Using Adamantane‐Based Dendrons

We have developed a straightforward strategy to multimerize an apoptogenic peptide that mimics the natural tumor necrosis factor‐related apoptosis‐inducing ligand (TRAIL) by using adamantane‐based dendrons as multivalent scaffolds. The selective binding affinity of the ligands to TRAIL receptor 2 (TR2) was studied by surface plasmon resonance, thus demonstrating that the trimeric and hexameric forms of the peptide exert an increased affinity of about 1500‐ and 20 000‐fold, respectively, relative to the monomer. Moreover, only the trimeric and hexameric ligands were able to induce cell death in TR2 expressing cells (BJAB), thus confirming that a multivalent form of the peptide is necessary to trigger a substantial TR2‐dependent apoptotic response in vitro. These results provide interesting insight into the multivalency effect on biological ligand/receptor interactions for future therapeutic applications.     

Photo‐Cross‐Linked Small‐Molecule Microarrays as Chemical Genomic Tools for Dissecting Protein–Ligand Interactions

We have developed a unique photo‐cross‐linking approach for immobilizing a variety of small molecules in a functional‐group‐independent manner. Our approach depends on the reactivity of the carbene species generated from trifluoromethylaryldiazirine upon UV irradiation. It was demonstrated in model experiments that the photogenerated carbenes were able to react with every small molecule tested, and they produced multiple conjugates in most cases. It was also found in on‐array immobilization experiments that various small molecules were immobilized, and the immobilized small molecules retained their ability to interact with their binding proteins. With this approach, photo‐cross‐linked microarrays of about 2000 natural products and drugs were constructed. This photo‐cross‐linked microarray format was found to be useful not merely for ligand screening but also to study the structure–activity relationship, that is, the relationship between the structural motif (or pharmacophore) found in small molecules and its binding affinity toward a protein, by taking advantage of the nonselective nature of the photo‐cross‐linking process.     

Chiroptical Detection of Nonchromophoric,Achiral Guests by Enantiopure Alleno‐Acetylenic Helicages

Enantiopure alleno‐acetylenic ligands assemble diastereoselectively upon the addition of a zinc(II) salt to form triple‐stranded helicates, which provide a sufficiently large helical cage (“helicage”) for the encapsulation of guests. The inclusion complexation of heteroalicycles is confirmed by ROESY and DOSY NMR spectroscopy and quantified in ¹H NMR binding titrations. The ECD spectra of the helicates, which showed strong Cotton effects and exciton coupling, were found to be extremely sensitive to the nature of the guest molecules. Consequently, a series of nonchromophoric, achiral guests of different sizes as well as regioisomers (1,3‐ and 1,4‐dioxane) became distinguishable on the basis of their induced CD (ICD) spectra. Molecular dynamics (MD) simulations show the adaptability of the cavity size to individual guest molecules and support the selective ICD output. Particularly high affinity towards 1,4‐dioxane allowed its selective detection at parts‐per‐million (ppm) levels in aqueous solutions.     

Binding‐Induced DNA Nanomachines Triggered by Proteins and Nucleic Acids

We introduce the concept and operation of a binding‐induced DNA nanomachine that can be activated by proteins and nucleic acids. This new type of nanomachine harnesses specific target binding to trigger assembly of separate DNA components that are otherwise unable to spontaneously assemble. Three‐dimensional DNA tracks of high density are constructed on gold nanoparticles functionalized with hundreds of single‐stranded oligonucleotides and tens of an affinity ligand. A DNA swing arm, free in solution, is linked to a second affinity ligand. Binding of a target molecule to the two ligands brings the swing arm to AuNP and initiates autonomous, stepwise movement of the swing arm around the AuNP surface. The movement of the swing arm, powered by enzymatic cleavage of conjugated oligonucleotides, cleaves hundreds of oligonucleotides in response to a single binding event. We demonstrate three nanomachines that are specifically activated by streptavidin, platelet‐derived growth factor, and the Smallpox gene. Substituting the ligands enables the nanomachine to respond to other molecules. The new nanomachines have several unique and advantageous features over DNA nanomachines that rely on DNA self‐assembly.     

High‐Yield Excited Triplet States in Pentacene Self‐Assembled Monolayers on Gold Nanoparticles through Singlet Exciton Fission

One of the major drawbacks of organic‐dye‐modified self‐assembled monolayers on metal nanoparticles when employed for efficient use of light energy is the fact that singlet excited states on dye molecules can be easily deactivated by means of energy transfer to the metal surface. In this study, a series of 6,13‐bis(triisopropylsilylethynyl)pentacene–alkanethiolate monolayer protected gold nanoparticles with different particle sizes and alkane chain lengths were successfully synthesized and were employed for the efficient generation of excited triplet states of the pentacene derivatives by singlet fission. Time‐resolved transient absorption measurements revealed the formation of excited triplet states in high yield (172±26 %) by suppressing energy transfer to the gold surface.     

Point‐of‐Care Amperometric Testing of Diabetic Marker (HbA1c) Using Specific Electroactive Antibodies

Specific immune detection of glycated hemoglobin is still a great challenge owing to the small epitopic difference between Hemoglobin (Hb) and HbA1c. We report a new electrochemical immunoassay format for point of care testing of HbA1c. A conducting self‐assembled monolayer of mercaptophenyl boronic acid (MPBA) was used as a capture layer for binding of glycated proteins and ferrocene tagged anti‐HbA1c antibody (FcAb) as a tracer molecule on a gold screen printed electrode. Validation of the new HbA1c assay was carried out using 6 clinical samples with known HPLC values and a correlation coefficient of 98 % was observed.     

Mixed‐monolayer of N‐hydroxysuccinimide‐terminated cross‐linker and short alkanethiol to improve the efficiency of biomolecule binding for biosensing

The goal of this study was to use a novel surface chemistry for modifying gold surfaces to decrease the steric hindrance, minimize the nonspecific bindings while providing directed immobilization of proteins for advancing the transducer property and to provide a biosensing platform for surface plasmon resonance (SPR) applications. Mixed self‐assembled monolayers (mSAMs) were prepared using 3,3′‐Dithiodipropionic acid di (N‐hydroxysuccinimide ester) (DSP) and 6‐mercapto‐1‐hexanol (MCH) and the selected model proteins bovine serum albumin (BSA) and lysozyme were tested for binding efficiency. First, binding of these two proteins at constant concentration to different DSP:MCH mSAMs were compared to deduce the best molar ratio for forming mSAM using a continuous flow system coupled to SPR. Coincidently the maximum protein binding DSP:MCH mSAM were the same for both proteins. The change in Response Unit (∆RU) signal due to protein binding between DSP SAM and maximum protein binding DSP:MCH mSAM for lysozyme binding was more in comparison to BSA binding. Second, the effect of BSA and lysozyme concentration on binding efficiency to maximum protein binding DSP:MCH mSAM were compared and discussed. Lysozyme and BSA were shown to reach saturations on the same monolayer at concentrations of 5.7x10⁻⁵ and 8.96x10⁻⁶ [M] respectively, hence the molar ratio for limit concentrations is 6:1. The DSP SAM, MCH SAM, and DSP:MCH mSAMs where maximum and minimum protein binding occurs were also characterized with XPS and Attenuated total reflectance‐Fourier transform infrared (ATR‐FTIR) spectroscopy. Blank gold surface, maximum protein binding DSP:MCH mSAM and BSA immobilized DSP:MCH mSAM on gold surface were also investigated utilizing tapping mode AFM.     

Fast Epitope Mapping for the Anti‐MUC1 Monoclonal Antibody by Combining a One‐Bead‐One‐Glycopeptide Library and a Microarray Platform

Anti‐MUC1 monoclonal antibodies (mAbs) are powerful tools that can be used to recognize cancer‐related MUC1 molecules, the O‐glycosylation status of which is believed to affect binding affinity. We demonstrate the feasibility of using a rapid screening methodology to elucidate those effects. The approach involves i) “one‐bead‐one‐compound”‐based preparation of bilayer resins carrying glycopeptides on the shell and mass‐tag tripeptides coding O‐glycan patterns in the core, ii) on‐resin screening with an anti‐MUC1 mAb, iii) separating positive resins by utilizing secondary antibody conjugation with magnetic beads, and (iv) decoding the mass‐tag that is detached from the positive resins pool by using mass spectrometric analysis. We tested a small library consisting of 27 MUC1 glycopeptides with different O‐glycosylations against anti‐MUC1 mAb clone VU‐3C6. Qualitative mass‐tag analysis showed that increasing the number of glycans leads to an increase in the binding affinity. Six glycopeptides selected from the library were validated by using a microarray‐based assay. Our screening provides valuable information on O‐glycosylations of epitopes leading to high affinity with mAb.