RAMPED-UP NMR: multiplexed NMR-based screening for drug discovery

The crucial step in drug discovery is the identification of a lead compound from a vast chemical library by any number of screening techniques. NMR-based screening has the advantage of directly detecting binding of a compound to the target. The spectra resulting from these screens can also be very complex and difficult to analyze, making this an inefficient process. We present here a method, RAMPED-UP NMR, (Rapid Analysis and Multiplexing of Experimentally Discriminated Uniquely Labeled Proteins using NMR) which generates simple spectra which are easy to interpret and allows several proteins to be screened simultaneously. In this method, the proteins to be screened are uniquely labeled with one amino acid type. There are several benefits derived from this unique labeling strategy: the spectra are greatly simplified, resonances that are most likely to be affected by binding are the only ones observed, and peaks that yield little or no information upon binding are eliminated, allowing the analysis of multiple proteins easily and simultaneously. We demonstrate the ability of three different proteins to be analyzed simultaneously for binding to two different ligands. This method will have significant impact in the use of NMR spectroscopy for both the lead generation and lead optimization phases of drug discovery by its ability to increase screening throughput and the ability to examine selectivity. To the best of our knowledge, this is the first time in any format that multiple proteins can be screened in one tube.     

High throughput screening of library compounds against an oligonucleotide substructure of an RNA target

Approximately 300,000 compounds from selected libraries were screened against a subdomain of a hepatitis C viral (HCV) RNA using a high throughput flow injection mass spectrometry (FIA-MS) method with automated data storage and analysis. Samples contained 2 microM RNA target and 10 microM of each of up to ten ligands. Preliminary studies to optimize operational parameters used the binding of aminoglycosides to the A44 subdomain of bacterial RNA. Binding (confirmed by titration) and sensitivity were maximized within the constraints of the library and throughput. The mobile phase of 5 mM ammonium acetate in 50% isopropanol maintained the noncovalent complexes and provided good detection by electrospray mass spectrometry. Additionally, this composition maximized general solubility of the various classes of compounds including the oligonucleotide and organic library molecules. Cation adduction was insignificant in this screen although some solute and target dependent acetate adduction was observed. The ion trap mass spectrometer provided sufficient mass resolution to identify complexes of RNA with known components of the library. Converted mass spectral data (netCDF) were subjected to two types of statistical evaluation based on binding. The first algorithm identified noncovalent complexes that correlated with the molecular weights of the injected compounds. The second yielded the largest peak in the noncovalent complex region of the spectrum; this spectrum may or may not correlate with expected well components. Sixty-three compounds were confirmed to bind by more stringent secondary testing. Titrations, which were carried out with selected binding compounds, yielded a range of dissociation constants. Biological activity was observed for eleven confirmed binders.     

Electrochemical activity and morphology of human erythrocytes at optically transparent ITO electrode

The electrochemical activity of a suspension of human erythrocytes was found at potentials above +0.4 V. The limiting current of electrooxidation was found to linearly depend on the cell concentration in the suspension. The electrochemical activity of an erythrocyte suspension is accompanied by reversible changes in the cell morphology only in non-buffered media.     

Affinity NMR: decoding DNA binding

We have shown that affinity NMR can be used to edit a NMR spectrum so that ligands that have affinity to DNA can be observed in the presence of other nonbinding molecules. Diffusion encoded spectroscopy (DECODES) can be used to identify the binding ligands. We were able to identify Hoechst 33342 as binding to the Drew-Dickerson dodecamer d(CGCGAATTCGCG)2 in the presence of the nonbinding molecules adenine, adenosine, and thiamine. Affinity NMR appears to be readily applicable to DNA systems for the following reasons. (1) The relaxation rate of the DNA oligonucleotides is favorable, thus the signal intensity loss due to relaxation is not severe. (2) A comparison of the patterns of the DNA cross-peaks upon binding in the two-dimensional total correlation spectroscopy and correlation spectroscopy spectrum are easily performed, and the ligand signals in the two-dimensional DECODES spectrum can be readily identified. (3) The aromatic part of the DNA spectrum is devoid of 2D cross-peaks in these correlation spectra, greatly facilitating the interpretation of the bound ligand in the DECODES spectrum.     

1H NMR Self-Diffusion Study of Morphology and Structure of Polyvinyl Alcohol Cryogels

The multicomponent self-diffusion of the polyvinyl alcohol (PVA) cryogels prepared by a freezing-thawing treatment of aqueous and water-DMSO solutions of PVA has been studied with the NMR FT-PGSE method. The temperature dependencies of the self-diffusion coefficients, Ds, for the PVA chains have a maximum at 45 degrees C due to the syneresis of cryogels. They are quite different from the monotonous increase of Ds for the aqueous solutions of PVA. Evaluated apparent activation energies, Ea, of the self-diffusion for the PVA chains in the PVA solutions and cryogels in D2O are practically the same and equal 22-24 kJ/mol below the crucial point. The proton spin-lattice relaxation times, T1, of the PVA chain also coincide with one another for solutions and cryogels. This means that molecular packing in cryogels depends mainly on the dimensions of the ice and polymer microcrystallites formed by freezing the solution. Above the crucial point polymer compartments become firmer, and the chain mobility somewhat reduces. The strength of cryogels also increases along with growing the DMSO contents and decreases by the BSA addition. For estimation of the cryogel morphology, effects of the restricted diffusion of both the water and PVA in a q-space have been taken into account. By the introduction of DMSO to cryogels the solvent filled pores become smaller, and channels become much shorter. The diameter of the PVA filaments is similar to those for all the cryogels, but the length of filaments with D2O is twice that for cryogels with a mixed solvent. Entrapment of BSA in the cryogel matrix by preparation leads to the increase of an average diameter of the water filled pores and destroys molecular packing the cryogel. Copyright 1999 Academic Press.     

Local solvability of PDE with constant coefficients

The fundamental result of the paper consists in the following assertion: Let D be an open set in Rⁿ,f £ L₂(D), and let be a distribution in Rⁿ with a compact support, whose Fourier transform satisfies the condition

Solving multistage asset investment problems by the sample average approximation method

The vast size of real world stochastic programming instances requires sampling to make them practically solvable. In this paper we extend the understanding of how sampling affects the solution quality of multistage stochastic programming problems. We present a new heuristic for determining good feasible solutions for a multistage decision problem. For power and log-utility functions we address the question of how tree structures, number of stages, number of outcomes and number of assets affect the solution quality. We also present a new method for evaluating the quality of first stage decisions.