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 sp 3 -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. S mall-molecule probe-and drug-discovery activities in academia and the pharmaceutical industry often begin with highthroughput screening. Many thousands of small molecules are tested with the expectation that each has potential as a discovery lead. Thus, assembling or synthesizing compound collections for small-molecule screening represents an important step in discovery success, particularly when selecting among compounds from a variety of synthetic and natural sources. Unbiased methods to evaluate the assay performance of compounds from different sources, and to relate performance to chemical structure (defined by computed structural properties) (1, 2), can provide guidance to one element of more valuable small-molecule screening collections.Comparative analyses between compounds often involve cheminformatic analysis of compound structures (3-5) or retrospective analysis of compound performance by mining the literature (6-8) or historical data (9, 10). For example, intermediate molecular complexity has been suggested as theoretically preferable for drug leads (11), and this relationship is supported by evidence mined from historical data (9). In this study, we performed unbiased comparisons of compounds from natural and synthetic sources by first identifying compounds with unknown activities and then exposing them to a common assay platform. We identified a compound collection comprising three subsets: (i) 6,152 compounds from commercial sources that are representative of many common screening collections (commercial compounds; CC); (ii) 6,623 compounds assembled from the academic synthetic chemistry community using, e.g., diversity-oriented synthesis (diverse compounds; DC); and (iii) 2,477 naturally occurring compounds (natural products; NP). We then (i) analyzed distributions of stereochemical and shape complexity for each set;(ii) measured protein-binding activities of each membe...

ChemBank (http://chembank.broad.harvard.edu/) is a public, web-based informatics environment developed through a collaboration between the Chemical Biology Program and Platform at the Broad Institute of Harvard and MIT. This knowledge environment includes freely available data derived from small molecules and small-molecule screens and resources for studying these data. ChemBank is unique among small-molecule databases in its dedication to the storage of raw screening data, its rigorous definition of screening experiments in terms of statistical hypothesis testing, and its metadata-based organization of screening experiments into projects involving collections of related assays. ChemBank stores an increasingly varied set of measurements derived from cells and other biological assay systems treated with small molecules. Analysis tools are available and are continuously being developed that allow the relationships between small molecules, cell measurements, and cell states to be studied. Currently, ChemBank stores information on hundreds of thousands of small molecules and hundreds of biomedically relevant assays that have been performed at the Broad Institute by collaborators from the worldwide research community. The goal of ChemBank is to provide life scientists unfettered access to biomedically relevant data and tools heretofore available primarily in the private sector.

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.A central theme in applying cheminformatics to discovery chemistry is to relate synthetic decisions to consequences on both chemical structure and biological assay performance. Historically, such efforts focused on small sets of similar compounds, and single performance measurements (1-3), providing guidance to chemists in compound optimization against singletarget proteins or processes (4). However, additional methods are needed to judge large sets of compounds, such as those used in small-molecule screening. Progress toward more valuable screening collections (5) requires unbiased methods to evaluate diversity of assay performance for compound sets rather than performance of individual members.A widely used method to judge compounds for drug discovery is the "rule of 5" (RO5) (6), which predicts poor absorption or permeation for compounds that deviate from property-value constraints: H-bond donors (Hd) and acceptors (Ha), molecular weight (MW), and calculated partition coefficients (cLogP). Recent studies have attempted to refine such rules (7-9) and extend them to other goals (10-13), such as making leads or probes. Such property filters have been debated and reviewed (14-16), and their long-term impact on pharmaceutical research is starting to be analyzed (17, 18). Importantly, exceptions to these rules, including natural products (19-21), ...

Pancreatic beta-cell apoptosis is a critical event during the development of type-1 diabetes. The identification of small molecules capable of preventing cytokine-induced apoptosis could lead to avenues for therapeutic intervention. We developed a set of phenotypic cell-based assays designed to identify such small-molecule suppressors. Rat INS-1E cells were simultaneously treated with a cocktail of inflammatory cytokines and a collection of 2,240 diverse small molecules, and screened using an assay for cellular ATP levels. Forty-nine top-scoring compounds included glucocorticoids, several pyrazole derivatives, and known inhibitors of glycogen synthase kinase-3β. Two compounds were able to increase cellular ATP levels, reduce caspase-3 activity and nitrite production, and increase glucose-stimulated insulin secretion in the presence of cytokines. These results indicate that small molecules identified by this screening approach may protect beta cells from autoimmune attack, and may be good candidates for therapeutic intervention in early stages of type-1 diabetes.Type-1 diabetes is caused by the autoimmune destruction of insulin-producing beta cellsin the pancreas. Beta-cell apoptosis involves a set of signaling cascades initiated by interleukin-1β (IL-1β), interferon-γ (IFN-γ), and tumor necrosis factor-α (TNF-α) (1-3). IL-1β and TNF-α induce NFκB expression, and downstream activation of gene expression is thought to occur through nitric oxide (NO) signaling, which both increases endoplasmic reticulum stress-response pathways and decreases beta cell-specific functions (4,5). NO is a highly reactive molecule that inhibits the electron-transport chain, leading to decreases in glucose oxidation rates, ATP generation, and insulin production (6); cellular nitrite is more stable and serves as a surrogate marker for NO. NFκB activation and IFN-γ-induced STAT-1 signaling work together to effect beta-cell apoptosis, mainly involving the intrinsic apoptotic pathway in both rodents and humans (7). The downstream effector of this cascade, caspase-3, results in apoptosis and the loss of the ability to secrete insulin in response to glucose stimulation.Small molecules that increase beta-cell survival in the presence of cytokines could be of potential clinical benefit to early-stage type-1 diabetic patients. Previous studies have described small molecules with protective effects in the presence of cytokines (8,9); most of these molecules were discovered because of their antioxidant or anti-inflammatory effects. For example, resveratrol in the presence of cytokines results in restoration of viability (10), * Corresponding author bwagner@broadinstitute.org. Conflict of interest statementThe corresponding author declares there are no conflicts of interest. Here, we describe a phenotypic screening approach to systematically discover small molecules that increase beta-cell viability and function in the presence of cytokines. Using the rat beta-cell line INS-1E, we screened 2,240 diverse compounds for the ability to alter cel...

A small molecule capable of distinguishing the distinct states resulting from cellular differentiation would be of enormous value, for example, in efforts aimed at regenerative medicine. We screened a collection of fluorescent small molecules for the ability to distinguish the differentiated state of a mouse skeletal muscle cell line. High-throughput fluorescence-based screening of C2C12 myoblasts and myotubes resulted in the identification of six compounds with the desired selectivity, which was confirmed by high-content screening in the same cell states. The compound that resulted in the greatest fluorescence intensity difference between the cell states was used as the screening agent in a pilot screen of 84 kinase inhibitors, each present in four doses, for inhibition of myogenesis. Of the kinase inhibitors, 17 resulted in reduction of fluorescence at one or more concentrations; among the "hits" included known inhibitors of myogenesis, confirming that this compound is capable of detecting the differentiated myotube state. We suggest that the strategy of screening for screening agents reported here may be extended more broadly in the future.