S1P1-selective in vivo-active agonists from high-throughput screening: off-the-shelf chemical probes of receptor interactions, signaling, and fate

The essential role of the sphingosine 1-phosphate (S1P) receptor S1P(1) in regulating lymphocyte trafficking was demonstrated with the S1P(1)-selective nanomolar agonist, SEW2871. Despite its lack of charged headgroup, the tetraaromatic compound SEW2871 binds and activates S1P(1) through a combination of hydrophobic and ion-dipole interactions. Both S1P and SEW2871 activated ERK, Akt, and Rac signaling pathways and induced S1P(1) internalization and recycling, unlike FTY720-phosphate, which induces receptor degradation. Agonism with receptor recycling is sufficient for alteration of lymphocyte trafficking by S1P and SEW2871. S1P(1) modeling and mutagenesis studies revealed that residues binding the S1P headgroup are required for kinase activation by both S1P and SEW2871. Therefore, SEW2871 recapitulates the action of S1P in all the signaling pathways examined and overlaps in interactions with key headgroup binding receptor residues, presumably replacing salt-bridge interactions with ion-dipole interactions.     

The complex of a bivalent derivative of galanthamine with torpedo acetylcholinesterase displays drastic deformation of the active-site gorge: implications for structure-based drug design

Bifunctional derivatives of the alkaloid galanthamine, designed to interact with both the active site of the enzyme acetylcholinesterase (AChE) and its peripheral cation binding site, have been assayed with Torpedo californica AChE (TcAChE), and the three-dimensional structures of their complexes with the enzyme have been solved by X-ray crystallography. Differences were noted between the IC(50) values obtained for TcAChE and those for Electrophorus electricus AChE. These differences are ascribed to sequence differences in one or two residues lining the active-site gorge of the enzyme. The binding of one of the inhibitors disrupts the native conformation of one wall of the gorge, formed by the loop Trp279-Phe290. It is proposed that flexibility of this loop may permit the binding of inhibitors such as galanthamine, which are too bulky to penetrate the narrow neck of the gorge formed by Tyr121 and Phe330 as seen in the crystal structure.     

Coarse-grained rigid blob model for soft matter simulations

We have developed a coarse-grained multiscale molecular simulation method for soft matter systems that directly incorporates stereochemical information. We divide the material into disjoint groups of atoms or particles that move as separate rigid bodies; we call these groups "rigid blobs," hence the name coarse-grained rigid blob model. The method is enabled by the construction of transferable interblob potentials that approximate the net intermolecular interactions, as obtained from ab initio electronic structure calculations, other all-atom empirical potentials, experimental data, or any combination of the above. We utilize a multipolar expansion to obtain the interblob potential-energy functions. The series, which contains controllable approximations that allow us to estimate the errors, approaches the original intermolecular potential as the number of terms increases. Using a novel numerical algorithm, we can calculate the interblob potentials very efficiently in terms of a few interaction moment tensors. This reduces the labor well beyond what is required in standard molecular-dynamics calculations and allows large-scale simulations for temporal scales commensurate with characteristic times of nano- and mesoscale systems. A detailed derivation of the formulas is presented, followed by illustrative applications to several systems showing that the method can effectively capture realistic microscopic details and can easily extend to large-scale simulations.     

Relative energies of substituted benzene valence isomers

Ab initio calculations employing the STO-3G basis set are used to obtain the relative energies of the benzene valence isomers and some selected monosubstituted derivatives. We find that 3,3'-bicyclopropenyl, the least stable of the five (CH)₆ examined, is slightly more stable in the anti conformation than the gauche (Φ = 45°) conformation in agreement with experiment. Substituents are calculated to produce significant changes in the relative energies of the benzene valence isomers. The ground-state isomerization of 1-Dewar benzeneearbinyl cation to benzyl cation is more exothermic than the aromatization of Dewar benzene, but is, in contrast to the latter, symmetry-allowed.     

Shot noise sets the limit of quantification in electrochemical measurements

Detection of single molecules, particles, and rapid redox events is a challenge of electrochemical investigations and requires either an amplification strategy or significant averaging for the electrochemical current to exceed the noise level. We consider the minimum number of electrons required to reach the limit of quantification in these electrochemical measurements. A survey of the literature indicates that the state-of-the-art limit in current detection for different types of measurements (e.g. voltammetry, single-molecule redox cycling, ion channel recordings of single molecules, metal nanoparticle collision, and phase nucleation) is independent of the nature of the measurement and increases linearly with reciprocal response time, Δt^?1, over ～5 orders of magnitude (from ～10 to ～10⁶ s^?1). We demonstrate that the practical limit of quantification requires cumulative measurement of ～2100 electrons during Δt and is determined by statistics of counting electrons, that is, the shot noise in the current.     

Effects of As(III) binding on alpha-helical structure

As(III) displays a wide range of effects in cellular chemistry. Surprisingly, the structural consequences of arsenic binding to peptides and proteins are poorly understood. This study utilizes model alpha-helical peptides containing two cysteine (Cys) residues in various sequential arrangements and spatial locations to study the structural effects of arsenic binding. With i, and i + 1, i + 2, or i + 3 arrangements, CD spectroscopy shows that As(III) coordination causes helical destabilization when Cys residues are located at central or C-terminal regions of the helix. Interestingly, arsenic binding to i, i + 3 positions results in the elimination of helical structure and the formation of a relatively stable alternate fold. In contrast, helical stabilization is observed for peptides containing i, i + 4 Cys residues, with corresponding pseudo pairwise interaction energies (Delta G(pw) degrees) of -1.0 and -0.7 kcal/mol for C-terminal and central placements, respectively. Binding affinities and association rate constants show that As(III) binding is comparatively insensitive to the location of the Cys residues within these moderately stable helices. These data demonstrate that As(III) binding can be a significant modulator of helical secondary structure.     

A mesoporous non-precious metal boride system: synthesis of mesoporous cobalt boride by strictly controlled chemical reduction

Generating high surface area mesoporous transition metal boride is interesting because the incorporation of boron atoms generates lattice distortions that lead to the formation of amorphous metal boride with unique properties in catalysis. Here we report the first synthesis of mesoporous cobalt boron amorphous alloy colloidal particles using a soft template-directed assembly approach. Dual reducing agents are used to precisely control the chemical reduction process of mesoporous cobalt boron nanospheres. The Earth-abundance of cobalt boride combined with the high surface area and mesoporous nanoarchitecture enables solar-energy efficient photothermal conversion of CO₂ into CO compared to non-porous cobalt boron alloys and commercial cobalt catalysts.

Generating high surface area mesoporous transition metal boride is challenging but interesting because incorporation of boron atoms can generate lattice distortion to form amorphous metal boride which has unique properties in catalysis.     

Some graphs with small second eigenvalue

For any prime,p, we construct a Cayley graph on the group,G, of affine linear transformations ofℤ/pℤ of degree 2(p−1) and second eigenvalue with the following special property: the adjacency matrix of the graph is supported on the “blocks” associated to the trivial representation and the irreducible representation of sizep−1. SinceG is of orderp(p−1), the correspondingt-uniform Cayley hypergraph has essentially optimal second eigenvalue for this degree and size of the graph (see [2] for definitions). En route we give, for any integerk>1, a simple Cayley graph onp ^k nodes of degreep of second eigenvalue . The author wishes to acknowledge the National Science Foundation for supporting this research in part under Grant CCR-8858788, and the Office of Naval Research under Grant N00014-87-K-0467.     

Existence and positivity of solutions of a fourth-order nonlinear PDE describing interface fluctuations

We study the partial differential equation which arose originally as a scaling limit in the study of interface fluctuations in a certain spin system. In that application x lies in R, but here we study primarily the periodic case × R S¹. We establish existence, uniqueness, and regularity of solutions, locally in time, for positive initial data in H¹(S¹), and prove the existence of several families of Lyapunov functions for the evolution. From the latter we establish a sharp connection between existence globally in time and positivity preservation: if [0], T*) is a maximal half open interval of existence for a positive solution of the equation, with T* < ∞, then lim_tT* w(t,·) exists in C¹(S¹) but vanishes at some point. We show further that if T* > (1 + √3)/16π² √3 then T* = ∞ and lim_t∞ w(t,.) exists and is constant. We discuss also some explicit solutions and propose a generalization to higher dimensions. © 1994 John Wiley & Sons, Inc.