Computational Characterization of Binding of Small Molecule Inhibitors to HIV‐1 gp41

Developing orally available small molecule inhibitors of HIV‐1 fusion has attracted significant interest over many years. Frey had recently reported several synthetic compounds which are experimentally shown to inhibit cell‐cell fusion in the low micromolar range. We carried out computational study to help identify possible binding modes by docking these compounds onto the hydrophobic pocket on gp41 and to characterize structures of binding complexes. The detailed gp41‐molecule binding interactions and free energies of binding are obtained through molecular dynamics simulation and MM‐PBSA calculation. Specific molecular interactions in the gp41‐inhibitor complexes are identified. The present computational study complements the corresponding experimental investigation and helps establish a good starting point for further refinement of small molecular gp41 inhibitors.     

Synthetic Glycopolypeptides as Potential Inhibitory Agents for Dendritic Cells and HIV‐1 Trafficking

Multivalent binding is a key for many critical biological processes and unique recognition and specificity in binding enables many of different glycans and proteins to work in a great harmony within the human body. In this study, the binding kinetics of synthetic glycopolypeptides to the dendritic cell lectin DC‐SIGN and their inhibition potential for DC‐SIGN interactions with the gp120 envelope glycoprotein of HIV‐1 (gp120) are investigated.

     

Facile One‐Pot Synthesis of Functional Gold Nanoparticle–Polymer Hybrids Using Ionic Block Copolymers as a Nanoreactor

A highly versatile approach to fabricate functional gold nanoparticle (AuNP)‐polymer hybrids is demonstrated by employing sulfonated block copolymers. The 3–5 nm sized ionic domain of the sulfonated poly(styrene‐block‐methylbutylene) (S_nMB_m) copolymers can be utilized as a nanoreactor where the Au ions can be selectively sequestered and reduced to AuNPs using a simple photochemical method. The size of the AuNPs can be adjusted in fine‐steps from 2.0 ± 0.3 to 3.9 ± 0.5 nm by changing the sulfonation levels of the S_nMB_m copolymers. Remarkably, significantly improved methanol oxidation properties are achieved with the hybrid materials owing to the ion conducting–SO₃H groups and the interconnected network of AuNPs confined within the self‐assembled microstructures, which provides electronic conductivity.     

Rapid Cationization of Gold Nanoparticles by Two‐Step Phase Transfer

Cationic gold nanoparticles offer intriguing opportunities as drug carriers and building blocks for self‐assembled systems. Despite major progress on gold nanoparticle research in general, the synthesis of cationic gold particles larger than 5 nm remains a major challenge, although these species would give a significantly larger plasmonic response compared to smaller cationic gold nanoparticles. Herein we present the first reported synthesis of cationic gold nanoparticles with tunable sizes between 8–20 nm, prepared by a rapid two‐step phase‐transfer protocol starting from simple citrate‐capped particles. These cationic particles form ordered self‐assembled structures with negatively charged biological components through electrostatic interactions.     

Enantiomeric and Diastereomeric Self‐Assembled Multivalent Nanostructures: Understanding the Effects of Chirality on Binding to Polyanionic Heparin and DNA

A family of four self‐assembling lipopeptides containing Ala‐Lys peptides attached to a C₁₆ aliphatic chain were synthesised. These compounds form two enantiomeric pairs that bear a diastereomeric relationship to one another (C₁₆‐l ‐Ala‐l ‐Lys/C₁₆‐d ‐Ala‐d ‐Lys) and (C₁₆‐d ‐Ala‐l ‐Lys/C₁₆‐l ‐Ala‐d ‐Lys). These diastereomeric pairs have very different critical micelle concentrations (CMCs). The self‐assembled multivalent (SAMul) systems bind biological polyanions as a result of the cationic lysine groups on their surfaces. For heparin binding, there was no significant enantioselectivity, but there was a binding preference for the diastereomeric assemblies with lower CMCs. Conversely, for DNA binding, there was significant enantioselectivity for systems displaying d ‐lysine ligands, with a further slight preference for attachment to l ‐alanine, with the CMC being irrelevant.     

Exploratory Study on the RNA‐Binding Structural Motifs by Library Screening Targeting pre‐miRNA‐29 a

The metabolic stream of microRNA (miRNA) production, the so‐called maturation process of miRNAs, became one of important metabolic paths for drug‐targeting to modulate the expression of genes related to a number of diseases. We carried out discovery studies on small molecules binding to the precursor of miR‐29a (pre‐miR‐29a) from a chemical library containing 41 119 compounds (AQ library) by the fluorescent indicator displacement (FID) assay using the xanthone derivative X2SdiMe as a fluorescent indicator. The FID assay provided 1075 compounds, which showed an increase of fluorescence. These compounds were subsequently submitted to a binding analysis in a surface plasmon resonance (SPR) assay on a pre‐miR‐29a immobilized surface. 21 hit compounds were identified with a good reproducibility in the binding. These compounds have not been reported to bind to RNA until now and can be classified into two groups on the basis of the kinetics in the binding. To gain more information on the motif structures that could be necessary for the binding to pre‐miR‐29a, 19 substructures were selected from the hit compounds. The substructure library (SS library) which consisted of 362 compounds was prepared from the AQ library. An SPR assay of the SS library on pre‐miR‐29a‐immobilized surface suggested that five substructures could potentially be important structural motifs to bind to pre‐miR‐29a. These studies demonstrate that the combination of FID‐based screening of chemical library and subsequent SPR assay would be one way for obtaining practical solutions for the discovery of molecules which bind to the target pre‐miRNAs.     

Toward the Rational Design of Galactosylated Glycoclusters That Target Pseudomonas aeruginosa Lectin A (LecA): Influence of Linker Arms That Lead to Low‐Nanomolar Multivalent Ligands

Anti‐infectious strategies against pathogen infections can be achieved through antiadhesive strategies by using multivalent ligands of bacterial virulence factors. LecA and LecB are lectins of Pseudomonas aeruginosa implicated in biofilm formation. A series of 27 LecA‐targeting glycoclusters have been synthesized. Nine aromatic galactose aglycons were investigated with three different linker arms that connect the central mannopyranoside core. A low‐nanomolar (K_d=19 nm , microarray) ligand with a tyrosine‐based linker arm could be identified in a structure–activity relationship study. Molecular modeling of the glycoclusters bound to the lectin tetramer was also used to rationalize the binding properties observed.     

Naphthyridine‐Benzoazaquinolone: Evaluation of a Tricyclic System for the Binding to (CAG)n Repeat DNA and RNA

The expansion of CAG repeats in the human genome causes the neurological disorder Huntington's disease. The small‐molecule naphthyridine‐azaquinolone NA we reported earlier bound to the CAG/CAG motif in the hairpin structure of the CAG repeat DNA. In order to investigate and improve NA ‐binding to the CAG repeat DNA and RNA, we conducted systematic structure‐binding studies of NA to CAG repeats. Among the five new NA derivatives we synthesized, surface plasmon resonance (SPR) assay showed that all of the derivatives modified from amide linkages in NA to a carbamate linkage failed to bind to CAG repeat DNA and RNA. One derivative, NBzA , modified by incorporating an additional ring to the azaquinolone was found to bind to both d(CAG)₉ and r(CAG)₉. NBzA binding to d(CAG)₉ was similar to NA binding in terms of large changes in the SPR assay and circular dichroism (CD) as well as pairwise binding, as assessed by electron spray ionization time‐of‐flight (ESI‐TOF) mass spectrometry. For the binding to r(CAG)₉, both NA and NBzA showed stepwise binding in ESI‐TOF MS, and NBzA ‐binding to r(CAG)₉ induced more extensive conformational change than NA ‐binding. The tricyclic system in NBzA did not show significant effects on the binding, selectivity, and translation, but provides a large chemical space for further modification to gain higher affinity and selectivity. These studies revealed that the linker structure in NA and NBzA was suitable for the binding to CAG DNA and RNA, and that the tricyclic benzoazaquinolone did not interfere with the binding.     

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.     

Oxidation Ability of Plasmon‐Induced Charge Separation Evaluated on the Basis of Surface Hydroxylation of Gold Nanoparticles

The oxidation ability of plasmonic photocatalysts, which has its origins in plasmon‐induced charge separation and has not yet been studied quantitatively and systematically, is important for designing practical photocatalytic systems. Oxidation ability was investigated on the basis of surface hydroxylation of Au nanoparticles on TiO₂ at various irradiation wavelengths and electrolyte pH values. The reaction proceeds only when the sum of the flat band potential of TiO₂ and the irradiated photon energy is close to, or more positive than, the theoretical potential for the reaction.     

Ag/AgCl@Cotton‐fabric:A Highly Stable and Easy‐recycling Plasmonic Photocatalyst under Visible Light Irradiation

Ag/AgCl@cotton‐fabric plasmonic photocatalyst has been synthesized by a facile method, which exhibits excellent stability for the decomposition of RhB and conveniency in the separation and recovery of the catalyst from the solution.     

Surface Plasmon Resonance Microscopy: From Single‐Molecule Sensing to Single‐Cell Imaging

Surface plasmon resonance microscopy (SPRM) is a versatile platform for chemical and biological sensing and imaging. Great progress in exploring its applications, ranging from single‐molecule sensing to single‐cell imaging, has been made. In this Minireview, we introduce the principles and instrumentation of SPRM. We also summarize the broad and exciting applications of SPRM to the analysis of single entities. Finally, we discuss the challenges and limitations associated with SPRM and potential solutions.     

Oxadiazole‐2‐thiol Adsorption on Gold Nanorods: A Joint Theoretical and Experimental Study by Using SERS,XPS, and DFT

The chemisorption of 1,3,4‐oxadiazole‐2‐thiol (ODT) on gold nanorods has been investigated by using surface‐enhanced Raman spectroscopy (SERS) and density functional theory (DFT). Although most of the SERS spectra have remarkable similarity to the normal Raman spectra of the pure analyte, the adsorption of ODT on a gold surface leads to a drastic change in its Raman spectrum and distinct vibrational features are obtained with gold nanorods and spherical nanoparticles. Simulated Raman spectra for hybrid systems that consist of an oxadiazole moiety coordinated to a Au₂₀ gold cluster provided valuable information about the coordination mode and enabled us to assign vibration modes.     

Determination of the Degree of Charge‐Transfer Contributions to Surface‐Enhanced Raman Spectroscopy

We explore the application of a previously suggested formula for determining the degree of charge transfer in surface‐enhanced Raman scattering (SERS). SERS is often described as a phenomenon which obtains its enhancement from three major sources, namely the surface plasmon resonance, charge‐transfer resonances as well as possible molecular resonances. At any chosen excitation wavelength, it is possible to obtain contributions from several sources and this has led to considerable confusion. The formula for the degree of charge transfer enables one to separate these effects, but it requires that spectra be obtained either at two or more different excitation wavelengths or as a function of applied potential. We apply this formula to several examples, which display rather large charge‐transfer contributions to the spectrum. These are p‐aminothiophenol (PATP), tetracyano‐ ethylene (TCNE) and piperidine. In PATP we can show that several lines of the same symmetry give the same degree of charge transfer. In TCNE we are able to identify the charge‐transfer transition, which contributes to the effect, and are able to independently determine the degree of charge transfer by wavenumber shifts. This enables a comparison of the two techniques of measurement. In piperidine, we present an example of molecule to metal charge transfer and show that our definition of charge transfer is independent of direction.