J. Anthony Wilson

Small molecules of different origins have distinct distributions of structural complexity that correlate with protein-binding profiles

Using a diverse collection of small molecules generated from a variety of sources, we measured protein-binding activities of each individual compound against each of 100 diverse (sequence-unrelated) proteins using small-molecule microarrays. We also analyzed structural features, including complexity, of the small molecules. We found that compounds from different sources (commercial, academic, natural) have different protein-binding behaviors and that these behaviors correlate with general trends in stereochemical and shape descriptors for these compound collections. Increasing the content of sp3-hybridized and stereogenic atoms relative to compounds from commercial sources, which comprise the majority of current screening collections, improved binding selectivity and frequency. The results suggest structural features that synthetic chemists can target when synthesizing screening collections for biological discovery. Because binding proteins selectively can be a key feature of high-value probes and drugs, synthesizing compounds having features identified in this study may result in improved performance of screening collections.

Spatial and temporal receptive fields of geniculate and cortical cells and directional selectivity

The spatio-temporal receptive fields (RFs) of cells in the macaque monkey lateral geniculate nucleus (LGN) and striate cortex (V1) have been examined and two distinct sub-populations of non-directional V1 cells have been found: those with a slow largely monophasic temporal RF, and those with a fast very biphasic temporal response. These two sub-populations are in temporal quadrature, the fast biphasic cells crossing over from one response phase to the reverse just as the slow monophasic cells reach their peak response. The two sub-populations also differ in the spatial phases of their RFs. A principal components analysis of the spatio-temporal RFs of directional V1 cells shows that their RFs could be constructed by a linear combination of two components, one of which has the temporal and spatial characteristics of a fast biphasic cell, and the other the temporal and spatial characteristics of a slow monophasic cell. Magnocellular LGN cells are fast and biphasic and lead the fast-biphasic V1 subpopulation by 7 ms; parvocellular LGN cells are slow and largely monophasic and lead the slow monophasic V1 sub-population by 12 ms. We suggest that directional V1 cells get inputs in the approximate temporal and spatial quadrature required for motion detection by combining signals from the two non-directional cortical sub-populations which have been identified, and that these sub-populations have their origins in magno and parvo LGN cells, respectively.

Route to three-dimensional fragments using diversity-oriented synthesis

Fragment-based drug discovery (FBDD) has proven to be an effective means of producing high-quality chemical ligands as starting points for drug-discovery pursuits. The increasing number of clinical candidate drugs developed using FBDD approaches is a testament of the efficacy of this approach. The success of fragment-based methods is highly dependent on the identity of the fragment library used for screening. The vast majority of FBDD has centered on the use of sp2-rich aromatic compounds. An expanded set of fragments that possess more 3D character would provide access to a larger chemical space of fragments than those currently used. Diversity-oriented synthesis (DOS) aims to efficiently generate a set of molecules diverse in skeletal and stereochemical properties. Molecules derived from DOS have also displayed significant success in the modulation of function of various “difficult” targets. Herein, we describe the application of DOS toward the construction of a unique set of fragments containing highly sp3-rich skeletons for fragment-based screening. Using cheminformatic analysis, we quantified the shapes and physical properties of the new 3D fragments and compared them with a database containing known fragment-like molecules.

Toward performance-diverse small-molecule libraries for cell-based phenotypic screening using multiplexed high-dimensional profiling

Significance A large compound screening collection is usually constructed to be tested in many distinct assays, each one designed to find modulators of a different biological process. However, it is generally not known to what extent a compound collection actually contains molecules with distinct biological effects (or even any effect) until it has been tested for a couple of years. This study explores a cost-effective way of rapidly assessing the biological performance diversity of a screening collection in a single assay. By simultaneously measuring a large number of cellular features, unbiased profiling assays can distinguish compound effects with high resolution and thus measure performance diversity. We show that this approach could be used as a filtering strategy to build effective screening collections. High-throughput screening has become a mainstay of small-molecule probe and early drug discovery. The question of how to build and evolve efficient screening collections systematically for cell-based and biochemical screening is still unresolved. It is often assumed that chemical structure diversity leads to diverse biological performance of a library. Here, we confirm earlier results showing that this inference is not always valid and suggest instead using biological measurement diversity derived from multiplexed profiling in the construction of libraries with diverse assay performance patterns for cell-based screens. Rather than using results from tens or hundreds of completed assays, which is resource intensive and not easily extensible, we use high-dimensional image-based cell morphology and gene expression profiles. We piloted this approach using over 30,000 compounds. We show that small-molecule profiling can be used to select compound sets with high rates of activity and diverse biological performance.

Quantifying structure and performance diversity for sets of small molecules comprising small-molecule screening collections

Using a diverse collection of small molecules we recently found that compound sets from different sources (commercial; academic; natural) have different protein-binding behaviors, and these behaviors correlate with trends in stereochemical complexity for these compound sets. These results lend insight into structural features that synthetic chemists might target when synthesizing screening collections for biological discovery. We report extensive characterization of structural properties and diversity of biological performance for these compounds and expand comparative analyses to include physicochemical properties and three-dimensional shapes of predicted conformers. The results highlight additional similarities and differences between the sets, but also the dependence of such comparisons on the choice of molecular descriptors. Using a protein-binding dataset, we introduce an information-theoretic measure to assess diversity of performance with a constraint on specificity. Rather than relying on finding individual active compounds, this measure allows rational judgment of compound subsets as groups. We also apply this measure to publicly available data from ChemBank for the same compound sets across a diverse group of functional assays. We find that performance diversity of compound sets is relatively stable across a range of property values as judged by this measure, both in protein-binding studies and functional assays. Because building screening collections with improved performance depends on efficient use of synthetic organic chemistry resources, these studies illustrate an important quantitative framework to help prioritize choices made in building such collections.

Multiplex Cytological Profiling Assay to Measure Diverse Cellular States

Computational methods for image-based profiling are under active development, but their success hinges on assays that can capture a wide range of phenotypes. We have developed a multiplex cytological profiling assay that “paints the cell” with as many fluorescent markers as possible without compromising our ability to extract rich, quantitative profiles in high throughput. The assay detects seven major cellular components. In a pilot screen of bioactive compounds, the assay detected a range of cellular phenotypes and it clustered compounds with similar annotated protein targets or chemical structure based on cytological profiles. The results demonstrate that the assay captures subtle patterns in the combination of morphological labels, thereby detecting the effects of chemical compounds even though their targets are not stained directly. This image-based assay provides an unbiased approach to characterize compound- and disease-associated cell states to support future probe discovery.

Expanding Stereochemical and Skeletal Diversity Using Petasis Reactions and 1,3-Dipolar Cycloadditions

A short and modular synthetic pathway using intramolecular 1,3-dipolar cycloaddition reactions and yielding functionalized isoxazoles, isoxazolines, and isoxazolidines is described. The change in shape of previous compounds and those in this study is quantified and compared using principal moment-of-inertia shape analysis.

Integration of differing chromaticities in early and midlevel spatial vision

Using Glass patterns composed of isoluminant dots we have investigated the segregation and integration of chromatic information by the visual system. By measuring pattern detection when the chromaticities of the two elements forming a dot pair are varied (intradipole variation), we characterize integration at an early level of spatial processing. By measuring pattern detection for dot pairs where the within-pair chromaticity is the same but the among-pair chromaticities are varied (interdipole variation) we characterize integration and segregation for a more global, midlevel, spatial processing mechanism. Using isoluminant patterns in which all dots have the same chromaticity, we find that (i) detection thresholds are similar to those for luminance-defined dots, and (ii) an equivalent-contrast metric approximately equates thresholds for various chromaticities, including those along both the cardinal and the intermediate axes of an opponent-color space. When intradipole chromaticity is varied we observe that (i) the ability of visual mechanisms to extract oriented dot pairs decreases with increasing chromaticity differences, and (ii) average bandwidths are similar for cardinal and intermediate directions. For pattern detection with interdipole chromatic variation the visual system does not segregate noise dot pairs from correlated dot pairs on the basis of chromatic differences alone, and appears to integrate oriented dot pairs of differing chromaticities in forming a global percept, even for large color differences. Isoluminant Glass patterns with translational and concentric correlations give similar results. The results are compared with those obtained for contrast variation in luminance-defined Glass Patterns and are discussed in terms of current multistage models of color processing by the visual system.