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Libraries

Chemical Screening

The Pathway Discovery Resource (PDR) has three compound libraries available for screening.  The Prestwick is the smallest library consisting of 1280 100% approved and marketed drugs.  The Spectrum is a small collectioSpectrum imagen of 2320 compounds that contains natural products and marketed and experimental drugs.  The Chembridge is a larger scale collection for hit and lead identification containing 20,000 diverse chemical structures.  We recommend that new investigators begin with a 2000 compound screen of the spectrum collection for assay validation and to generate preliminary data to be followed up with a larger scale screen to identify highly potent compounds.

1. The Spectrum Collection

The 2320 compounds in the SPECTRUM Collection were selected by medicinal chemists and biologists so as to provide a wide range of biological activities and structural diversity for screening programs with special emphasis on the de-novo assays emerging today. Such content provides the opportunity to evaluate drugs and biochemical tools with known biological profiles and, at the same time, explore the potential of novel structural and topographical diversity manifest in pure natural products. Each compound has a minimum of 95% purity.  Below are the components. 

The Drug Components (60%)
Drugs that have been introduced in the US (1280 compounds with USAN/USP designations) predominate. Also included are 320 drugs that are limited in use to Europe (INN & BAN) and Japan (JAN).

The Natural Products (25%)
The remainder of the SPECTRUM collection includes 640 additional pure natural products with unknown biological properties, which are derived from natural sources worldwide. Many of these are isolated and purified in our laboratories or those of our affiliates, Gaia Chemical Corporation and Planta Analytica LLC. These compounds are selected on the basis of chemical class and structural diversity.

Other Bioactive Components (15%)
Representatives of non-drug enzyme inhibitors, receptor blockers, membrane active compounds, and cellular toxins are provided in the SPECTRUM collection. Many of these 420 compounds have either not reached development or been dropped for toxicological or other reasons. Also included are representatives of marketed pesticides and herbicides for comparative purposes. These diverse compounds are important assets in defining the scope of your assay and, once again, may reflect an unforeseen activity.

References to the use of the Spectrum Collection

  • DA Kocisko, GS Baron, R Rubenstein, J Chen, S Kuizon, B Caughey, New Inhibitors of Scrapie-Associated Prion Protein Formation in a Library of 2,000 Drugs and Natural Products, J Virology 77: 10288 (2003).
  • C Weissmann, A Aguzzi, Approaches To Therapy Of Prion Diseases, Ann Rev Med 56: 321 (2005).
  • H Sun, X Liu, Q Xiong, S Shikano and M Li, Chronic Inhibition of Cardiac Kir2.1 and hERG Potassium Channels by Celastrol with Dual effects on Both Ion Conductivity and Protein Trafficking, J Biol Chem 281:5877 (2006)
  • JL Weisman, AP Liou, AA Shelat, FE Cohen, RK Guy and JL DeRisi, Searching for New Antimalarial Therapeutics amongst Known Drugs, Chem Biol & Drug Design, 67:409 (2006)
  • M Stallings-Mann, L Jamieson, RP Regala, C Weems, NR Murray and AP Fields, A Novel Small-Molecule Inhibitor of Protein Kinase C Blocks Transformed Growth of Non-Small-Cell Lung Cancer Cells, Cancer Research 66:1767 (2006)

2. Chembridge Diversity Set

Chembridge diversity setWe currently have 20,000 randomly selected molecules from Chembridge’s DIVERset library.  This compound collection was selected from the 450,000 compound library to represent structural diversity within the larger library.  Hits can be followed up for structure activity analysis or identification of higher quality leads by computational similarity searching of the larger library for compounds with related structural features.

DIVERSet™ - A "universally" diverse collection of 50,000 drug-like small molecules. The set is rationally selected based on 3D pharmacophore analysis to cover the broadest part of biologically relevant pharmacophore diversity space. A highly recognized and proven primary screening tool for a wide range of both validated and new biological targets.

3. Prestwick Library

Prestwick library imageThe Prestwick Chemical Library® contains 1120 small molecules, 90% being marketed drugs and 10% bioactive alkaloids or related substances, thus it presents the greatest possible degree of drug-likeliness. The active compounds were selected for their high chemical and pharmacological diversity as well as for their known bioavailability and safety in humans. The Prestwick Chemical Library ® was designed to reduce the risk of "low quality" hits, reduce the cost of the initial screening, and accelerate lead discovery.

siRNA Screening

The Pathway Discovery Resource (PDR) currently offers siRNA screening of the human genome with Ambion’s Silence Select Human Genome siRNA Library v4 (Catalog # 4397926). 

Human Genome siRNA Library
(Comprised of Part Numbers: 4397922 + 4397923 + 4397924)
Increasingly, researchers are performing genome scale surveys of gene function. TheSilencer® Select Human Genome siRNA Library V4 is ideal for this purpose. Three unique, non-overlapping siRNAs are provided for each of 21,584 human targets. The siRNAs targeting the “druggable" portion of this library are arranged by gene functional class to enable easy screening of important gene subsets such as kinase, phosphatase, GPCR, etc. This siRNA library is supplied in 384-well plates.