Fabrication of Highly Stable Glyco‐Gold Nanoparticles and Development of a Glyco‐Gold Nanoparticle‐Based Oriented Immobilized Antibody Microarray for Lectin (GOAL) Assay

The design of high‐affinity lectin ligands is critical for enhancing the inherently weak binding affinities of monomeric carbohydrates to their binding proteins. Glyco‐gold nanoparticles (glyco‐AuNPs) are promising multivalent glycan displays that can confer significantly improved functional affinity of glyco‐AuNPs to proteins. Here, AuNPs are functionalized with several different carbohydrates to profile lectin affinities. We demonstrate that AuNPs functionalized with mixed thiolated ligands comprising glycan (70 mol %) and an amphiphilic linker (30 mol %) provide long‐term stability in solutions containing high concentrations of salts and proteins, with no evidence of nonspecific protein adsorption. These highly stable glyco‐AuNPs enable the detection of model plant lectins such as Concanavalin A, wheat germ agglutinin, and Ricinus communis Agglutinin 120, at subnanomolar and low picomolar levels through UV/Vis spectrophotometry and dynamic light scattering, respectively. Moreover, we develop in situ glyco‐AuNPs‐based agglutination on an oriented immobilized antibody microarray, which permits highly sensitive lectin sensing with the naked eye. In addition, this microarray is capable of detecting lectins presented individually, in other environmental settings, or in a mixture of samples. These results indicate that glyconanoparticles represent a versatile and highly sensitive method for detecting and probing the binding of glycan to proteins, with significant implications for the construction of a variety of platforms for the development of glyconanoparticle‐based biosensors.     

Structural informatics,modeling, and design with an open‐source Molecular Software Library (MSL)

We present the Molecular Software Library (MSL), a C++ library for molecular modeling. MSL is a set of tools that supports a large variety of algorithms for the design, modeling, and analysis of macromolecules. Among the main features supported by the library are methods for applying geometric transformations and alignments, the implementation of a rich set of energy functions, side chain optimization, backbone manipulation, calculation of solvent accessible surface area, and other tools. MSL has a number of unique features, such as the ability of storing alternative atomic coordinates (for modeling) and multiple amino acid identities at the same backbone position (for design). It has a straightforward mechanism for extending its energy functions and can work with any type of molecules. Although the code base is large, MSL was created with ease of developing in mind. It allows the rapid implementation of simple tasks while fully supporting the creation of complex applications. Some of the potentialities of the software are demonstrated here with examples that show how to program complex and essential modeling tasks with few lines of code. MSL is an ongoing and evolving project, with new features and improvements being introduced regularly, but it is mature and suitable for production and has been used in numerous protein modeling and design projects. MSL is open‐source software, freely downloadable at http://msl‐libraries.org . We propose it as a common platform for the development of new molecular algorithms and to promote the distribution, sharing, and reutilization of computational methods. © 2012 Wiley Periodicals, Inc.     

Structure‐based redesign of proteins for minimal T‐cell epitope content

The protein universe displays a wealth of therapeutically relevant activities, but T‐cell driven immune responses to non‐“self” biological agents present a major impediment to harnessing the full diversity of these molecular functions. Mutagenic T‐cell epitope deletion seeks to mitigate the immune response, but can typically address only a small number of epitopes. Here, we pursue a “bottom‐up” approach that redesigns an entire protein to remain native‐like but contain few if any immunogenic epitopes. We do so by extending the Rosetta flexible‐backbone protein design software with an epitope scoring mechanism and appropriate constraints. The method is benchmarked with a diverse panel of proteins and applied to three targets of therapeutic interest. We show that the deimmunized designs indeed have minimal predicted epitope content and are native‐like in terms of various quality measures, and moreover that they display levels of native sequence recovery comparable to those of non‐deimmunized designs. © 2013 Wiley Periodicals, Inc.     

Glycopolymers and Glyco‐nanoparticles in Biomolecular Recognition Processes and Vaccine Development

With advances in polymerization techniques as well as selective chemical modification of carbohydrates, glycopolymers and glyco‐nanoparticles are emerging as an important class of materials with tailored properties or novel nanotechnology‐based platforms for a number of applications. The field of the so‐called glyco‐nanotechnology is starting to show some promises for future clinical applications. Glyco‐nanoparticles, due to their versatile nature, could offer a platform for the design of carbohydrate‐based vaccines and possibly allow the development of new single‐dose vaccines in disease areas of unmet need. This paper surveys the emerging roles of carbohydrate‐based polymeric and nanomaterials for biomolecular recognition processes and vaccine development.

     

Prediction of Protein Structure Using Surface Accessibility Data

An approach to the de novo structure prediction of proteins is described that relies on surface accessibility data from NMR paramagnetic relaxation enhancements by a soluble paramagnetic compound (sPRE). This method exploits the distance‐to‐surface information encoded in the sPRE data in the chemical shift‐based CS‐Rosetta de novo structure prediction framework to generate reliable structural models. For several proteins, it is demonstrated that surface accessibility data is an excellent measure of the correct protein fold in the early stages of the computational folding algorithm and significantly improves accuracy and convergence of the standard Rosetta structure prediction approach.     

Induced Fit of C2H2 in a Flexible MOF Through Cooperative Action of Open Metal Sites

Porous materials that can undergo pore‐structure adjustment to better accommodate specific molecules are ideal for separation and purification. Here, we report a stable microporous metal‐organic framework, JNU‐1, featuring one‐dimensional diamond‐shaped channels with a high density of open metal sites arranged on the surface for the cooperative binding of acetylene. Together with its framework flexibility and appropriate pore geometry, JNU‐1 exhibits an induced‐fit behavior for acetylene. The specific binding sites and continuous framework adaptation upon increased acetylene pressure are validated by molecular modeling and in situ X‐ray diffraction study. This unique induced‐fit behavior endows JNU‐1 with an unprecedented increase in the acetylene binding affinity (adsorption enthalpy: up to 47.6 kJ mol^?1 at ca. 2.0 mmol g^?1 loading).     

The diversity in the applications of partial least squares: an overview

Advances in technology make it happen to have massive amount of information in the form of multiple variables per object. The use of multivariate approaches for modeling the real‐life phenomena is natural in such situation. There are numerous multivariate approaches in the literature, and its a challenge to stay updated on the possibilities. Partial least squares (PLSs) are one of the many modeling approaches for high‐throughput data, and its use in different fields to address the variety of problems has been increased in recent years. We therefore present an overview of PLS's applications. The objective of this paper is to give a comprehensive overview on the advances in PLS algorithm together with its applications for regression, classification, variable selection, and survival analysis problems covering genomics, chemometrics, neuroinformatics, process control, computer vision, econometric, environmental studies, and so on. We have mainly presented different PLS approaches and their applications, so that the reader can easily get an understanding of possibility to use PLS for their own field. For further reading, literature references together with software availability are provided. Copyright © 2015 John Wiley & Sons, Ltd.     

Synthesis and Surface‐Spectroscopic Characterization of Photoisomerizable glyco‐SAMs on Au(111)

Photoisomerizable glyco‐SAMs (self‐assembled monolayers), utilizing synthetic azobenzene glycoside derivatives were fabricated. The ultimate goal of this project is to assay the influence of the 3D arrangement of sugar ligands on cell adhesion, and eventually make cell adhesion photoswitchable. However, it is a prerequisite for any biological study on the spatial conditions of carbohydrate recognition, that photoisomerization of the surface molecules can be verified. Here, we employed IRRAS and XPS to spectroscopically characterize glyco‐SAMs. In particular and unprecedented to date, we prove reversible E→Z→E isomerization of azobenzene glycoside‐terminated SAMs.     

Grid‐based molecular footprint comparison method for docking and de novo design: Application to HIVgp41

Scoring functions are a critically important component of computer‐aided screening methods for the identification of lead compounds during early stages of drug discovery. Here, we present a new multigrid implementation of the footprint similarity (FPS) scoring function that was recently developed in our laboratory which has proven useful for identification of compounds which bind to a protein on a per‐residue basis in a way that resembles a known reference. The grid‐based FPS method is much faster than its Cartesian‐space counterpart, which makes it computationally tractable for on‐the‐fly docking, virtual screening, or de novo design. In this work, we establish that: (i) relatively few grids can be used to accurately approximate Cartesian space footprint similarity, (ii) the method yields improved success over the standard DOCK energy function for pose identification across a large test set of experimental co‐crystal structures, for crossdocking, and for database enrichment, and (iii) grid‐based FPS scoring can be used to tailor construction of new molecules to have specific properties, as demonstrated in a series of test cases targeting the viral protein HIVgp41. The method is available in the program DOCK6. © 2013 Wiley Periodicals, Inc.     

Two‐Photon Fluorescent Probes for Metal Ions

Two‐photon microscopy (TPM) has become an indispensible tool in biology and medicine owing to the capability of imaging the intact tissue for a long period of time. To make it a versatile tool in biology, a variety of two‐photon probes for specific applications are needed. In this context, many research groups are developing two‐photon probes for various applications. In this Focus Review, we summarize recent results on model studies and selected examples of two‐photon probes that can detect intracellular free metal ions in live cells and tissues to provide a guideline for the design of useful two‐photon probes for various in vivo imaging applications.     

Nanozeolite‐LTL with GdIII Deposited in the Large and EuIII in the Small Cavities as a Magnetic Resonance Optical Imaging Probe

The immense structural diversity of more than 200 known zeolites is the basis for the wide variety of applications of these fascinating materials ranging from catalysis and molecular filtration to agricultural uses. Despite this versatility, the potential of zeolites in medical imaging has not yet been much exploited. In this work a novel strategy is presented to selectively deposit different ions into distinct framework locations of zeolite‐LTL (Linde type L) and it is demonstrated that the carefully ion‐exchanged Gd/Eu‐containing nanocrystals acquire exceptional magnetic properties in combination with enhanced luminescence. This smart exploitation of the framework structure yields the highest relaxivity density (13.7 s^?1 L g^?1 at 60 MHz and 25 °C) reported so far for alumosilicates, rendering these materials promising candidates for the design of dual magnetic resonance/optical imaging probes, as demonstrated in preliminary phantom studies.     

Cooperative Hydrogen Bonding in Glyco–Oligoamides: DNA Minor Groove Binders in Aqueous Media

A strategy to create cooperative hydrogen‐bonding centers by using strong and directional intramolecular hydrogen‐bonding motifs that can survive in aqueous media is presented. In particular, glyco–oligoamides, a family of DNA minor groove binders, with cooperative and non‐cooperative hydrogen‐bonding donor centers in the carbohydrate residues have been designed, synthesized, and studied by means of NMR spectroscopy and molecular modeling methods. Indeed, two different sugar moieties, namely, β‐D ‐Man‐Py‐γ‐Py‐Ind ( 1 ; Ind=indole, Man=mannose, Py=pyrrole) and β‐D ‐Tal‐Py‐γ‐Py‐Ind ( 2 ; Tal=talose), were chosen according to our design. These sugar molecules should present one‐ or two‐directional intramolecular hydrogen bonds. The challenge has been to study the conformation of the glyco–oligoamides at low temperature in physiological media by detecting the exchangeable protons (amide NH and OH resonances) by means of NMR spectroscopic analysis. In addition, two more glyco–oligoamides with non‐cooperative hydrogen‐bonding centers, that is, β‐D ‐Glc‐Py‐γ‐Py‐Ind ( 3 ; Glc=glucose), β‐D ‐Gal‐Py‐γ‐Py‐Ind ( 4 ; Gal=galactose), and the model compounds β‐D ‐Man‐Py‐NHAc ( 5 ) and β‐D ‐Tal‐Py‐NHAc ( 6 ) were synthesized and studied for comparison. We have demonstrated the existence of directional intramolecular hydrogen bonds in 1 and 2 in aqueous media. The unexpected differences in terms of stabilization of the intramolecular hydrogen bonds in 1 and 2 relative to 5 and 6 promoted us to evaluate the influence of CH—π interactions on the establishment of intramolecular hydrogen bonds by using computational methods. Initial binding studies of 1 and 2 with calf‐thymus DNA and poly(dA‐dT)₂ by NMR spectroscopic analysis and molecular dynamics simulations were also carried out. Both new sugar–oligoamides are bound in the minor groove of DNA, thus keeping a stable hairpin structure, as in the free state, in which both intramolecular hydrogen‐bonding and CH—π interactions are present.     

High‐Silica Zeolite SSZ‐61 with Dumbbell‐Shaped Extra‐Large‐Pore Channels

The synthesis of the high‐silica zeolite SSZ‐61 using a particularly bulky polycyclic structure‐directing agent and the subsequent elucidation of its unusual framework structure with extra‐large dumbbell‐shaped pore openings are described. By using information derived from a variety of X‐ray powder diffraction and electron microscopy techniques, the complex framework structure, with 20 Si atoms in the asymmetric unit, could be determined and the full structure refined. The Si atoms at the waist of the dumbbell are only three‐connected and are bonded to terminal O atoms pointing into the channel. Unlike the six previously reported extra‐large‐pore zeolites, SSZ‐61 contains no heteroatoms in the framework and can be calcined easily. This, coupled with the possibility of inserting a catalytically active center in the channel between the terminal O atoms in place of H⁺, afford SSZ‐61 intriguing potential for catalytic applications.     

Fast docking using the CHARMM force field with EADock DSS

The prediction of binding modes (BMs) occurring between a small molecule and a target protein of biological interest has become of great importance for drug development. The overwhelming diversity of needs leaves room for docking approaches addressing specific problems. Nowadays, the universe of docking software ranges from fast and user friendly programs to algorithmically flexible and accurate approaches. EADock2 is an example of the latter. Its multiobjective scoring function was designed around the CHARMM22 force field and the FACTS solvation model. However, the major drawback of such a software design lies in its computational cost. EADock dihedral space sampling (DSS) is built on the most efficient features of EADock2, namely its hybrid sampling engine and multiobjective scoring function. Its performance is equivalent to that of EADock2 for drug‐like ligands, while the CPU time required has been reduced by several orders of magnitude. This huge improvement was achieved through a combination of several innovative features including an automatic bias of the sampling toward putative binding sites, and a very efficient tree‐based DSS algorithm. When the top‐scoring prediction is considered, 57% of BMs of a test set of 251 complexes were reproduced within 2 Å RMSD to the crystal structure. Up to 70% were reproduced when considering the five top scoring predictions. The success rate is lower in cross‐docking assays but remains comparable with that of the latest version of AutoDock that accounts for the protein flexibility. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011     

A Fully Synthetic Four‐Component Antitumor Vaccine Consisting of a Mucin Glycopeptide Antigen Combined with Three Different T‐Helper‐Cell Epitopes

In a new concept of fully synthetic vaccines, the role of T‐helper cells is emphasized. Here, a synthetic antitumor vaccine consisting of a diglycosylated tumor‐associated MUC1 glycopeptide as the B‐cell epitope was covalently cross‐linked with three different T‐helper‐cell epitopes via squaric acid ligation of two linear (glyco)peptides. In mice this four‐component vaccine administered without external immune‐stimulating promoters elicit titers of MUC1‐specific antibodies that were about eight times higher than those induced by a vaccine containing only one T‐helper‐cell epitope. The promising results indicate that multiple activation of different T‐helper cells is useful for applications in which increased immunogenicity is required. In personalized medicine, in particular, this flexible construction of a vaccine can serve as a role model, for example, when T‐helper‐cell epitopes are needed that match human leukocyte antigens (HLA) in different patients.     

Use of a tree‐structured hierarchical model for estimation of location and uncertainty in multivariate spatial data

Analysis and modeling of spatial data are of considerable interest in many applications. However, the prediction of geographical features from a set of chemical measurements on a set of geographically distinct samples has never been explored. We report a new, tree‐structured hierarchical model for the estimation of geographical location of spatially distributed samples from their chemical measurements. The tree‐structured hierarchical modeling used in this study involves a set of geographic regions stored in a hierarchical tree structure, with each nonterminal node representing a classifier and each terminal node representing a regression model. Once the tree‐structured model is constructed, given a sample with only chemical measurements available, the predicted regional location of the sample is gradually restricted as it is passed through a series of classification steps. The geographic location of the sample can be predicted using a regression model within the terminal subregion. We show that the tree‐structured modeling approach provides reasonable estimates of geographical region and geographic location for surface water samples taken across the entire USA. Further, the location uncertainty, an estimate of a probability that a test sample could be located within a pre‐estimated, joint prediction interval that is much smaller than the terminal subregion, can also be assessed. Copyright © 2014 John Wiley & Sons, Ltd.     

Glyco‐pseudopolyrotaxanes: Carbohydrate Wheels Threaded on a Polymer String and Their Inhibition of Bacterial Adhesion

We report glyco‐pseudopolyrotaxanes composed of cucurbit[6]uril‐based mannose wheels (ManCB[6]) threaded on polyviologen (PV), which not only effectively induce bacterial aggregation, but also exhibit high inhibitory activity against bacterial binding to host cells. Three glyco‐pseudopolyrotaxanes ( 1 – 3 ), which have 10, 5, and 3 ManCB[6] wheels, respectively, on a PV string, were prepared and characterized. Bacterial aggregation assays and hemagglutination inhibition assays illustrated the specific and multivalent interaction between the glyco‐pseudopolyrotaxanes and E. coli ORN178. Compound 3 was especially effective at inducing bacterial aggregation and showed 300 times higher inhibitory potency than monomeric methyl‐α‐mannoside (Me‐αMan) for ORN178‐induced hemagglutination. Furthermore, we demonstrated their inhibitory activities for the adhesion of ORN178 bacteria to urinary epithelial cells as a model of urinary tract infection. Our findings suggest that these supramolecular carbohydrate clusters are potentially useful in antiadhesion therapy.     

Multichromophores for Nonlinear Optics: Designing the Material Properties by Electrostatic Interactions

To fully exploit the promise of molecular materials for NLO applications, inter‐ and supramolecular interactions must be accounted for. We review our recent work on electrostatic interchromophore interactions in multichromophores for NLO applications. The discussion is based on a bottom‐up modeling strategy: each chromophore is described in terms of an essential state model, validated and parameterized against spectroscopic data for solvated chromophores. The relevant information is then used to build a model for clusters of chromophores interacting through electrostatic forces. Exact NLO responses and spectra calculated within this model fully account for collective and cooperative interchromophore interactions, which can either amplify or suppress NLO responses; supramolecular engineering of multichromophores is a powerful tool for the design of NLO materials. Moreover, new features emerge in multichromophores with no counterpart at the single‐chromophore level, offering new exciting opportunities for applications.