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Division of Program Coordination, Planning, and Strategic Initiatives (DPCPSI) National Institutes of Health  •  U.S. Department of Health and Human Services

Molecular Libraries and Imaging


Small molecules, often with molecular weights of 500 or below, have proven to be extremely important to researchers to explore function at the molecular, cellular, and in vivo level. Such molecules have also been proven to be valuable for treating diseases, and most medicines marketed today are from this class.

A key challenge is to identify small molecules effective at modulating a given biological process or disease state. Currently, researchers must systematically screen tens or hundreds of thousands of small molecules to find a successful match between a chemical and its target. This process is known as high-throughput screening or HTS. The capacity for HTS has been built within the pharmaceutical and biotechnology sectors for the purposes of drug development over the last ten years, but similar resources have not existed in the public sector.

The Molecular Libraries Roadmap offers public sector biomedical researchers access to the large-scale screening capacity necessary to identify small molecules that can be optimized as chemical probes to study the functions of genes, cells, and biochemical pathways. This will lead to new ways to explore the functions of genes and signaling pathways in health and disease.

NIH anticipates that these projects will also facilitate the development of new drugs, by providing early stage chemical compounds that will enable researchers in the public and private sectors to validate new drug targets, which could then move into the drug-development pipeline. This is particularly true for rare diseases, which may not be attractive for development by the private sector.

Three key technological advances drive NIH's effort to build small molecule libraries. First, the successful completion of the Human Genome Project has provided an enormous cache of human biology to be studied and potential drug targets to be discovered. Second, developments in chemistry have given researchers in the public sector the ability to rapidly and efficiently synthesize large numbers of related molecules, a capability previously available only to researchers in pharmaceutical and biotechnology companies. Third, advances in robotic technology and informatics now allow scientists to screen hundreds of thousands of compounds in a single day, an orders of magnitude greater capacity than was available a decade ago.

The Molecular Libraries Roadmap has three components:

  1. Molecular Libraries Probe Production Centers Network (MLPCN). This is a nationwide consortium of small molecule screening centers that has been recently funded to produce innovative chemical tools for use in biological research. The MLPCN performs HTS on assays provided by the research community, against a large library of small molecules maintained in a central molecule repository. The network also performs optimization chemistry required to produce useful in vitro chemical probes (research tools for the targets or phenotypes studied in the assays) from the “hits” identified in the initial screening. The MLPCN has established a collection of 300,000 chemically diverse small molecules some of which have known biological activities and others of which have the potential to modulate novel biological functions. Over time, this collection will be expanded and modified to provide a working set of molecules that will target larger domains of "biological space," which represents all of the biomolecular surface domains that can potentially interact with a small molecule. All of the results from the MLPCN’s activities will be placed into a public database called PubChem, and information about probe compounds will be made available to all researchers, in both public and private sectors, for their use in studying biology and disease.
  2. PubChem. A new and comprehensive database of chemical structures and their biological activities has been developed by the National Center for Biotechnology Information at NIH. PubChem houses both compound information from the scientific literature as well as screening and probe data from the MLPCN.
  3. Technology Development. As was the case with the Human Genome Project at its inception, the ultimate goal of the Molecular Libraries Roadmap – a comprehensive set of small molecule modulators of a majority of the genes and functions of humans and other organisms – is unachievable with current technologies. Therefore, 30 percent of the Molecular Libraries Roadmap budget is devoted to technology development in the following three areas:

    • Chemical Diversity. This area supports the development of new and diverse chemical libraries for screening in the MLPCN centers, as well as new methods for producing, isolating, characterizing, and modifying natural products.
    • Assay diversity. This area supports the development of a continuously evolving stream of scientifically novel and technologically outstanding assays that can be automated and used for screening small molecules within the Molecular Libraries Probe Production Centers Network. The aim of this effort is to enable the design of pharmacologic tools to explore cellular and physiological function.
    • Instrumentation. This area supports the development of new methods for high-throughput measurement of novel biological assays.

The Molecular Libraries and Imaging Roadmap also enhance the discovery and availability of small molecules for molecular imaging. This includes imaging of molecules or molecular events in biological systems that span the scale from single cells to whole organisms. Ultimately, it is hoped that this effort will enable personalized profiles of cell and tissue function, which may lead to more individualized approaches to diagnosing and treating disease. By significantly enhancing the support of this emerging field, NIH will ensure that molecular imaging will become a powerful tool for biomedical research and will be a synergistic component of research in molecular medicine that promises landmark improvements in clinical care.

The Molecular Imaging Roadmap has two components:

  1. Molecular Imaging and Contrast Agent Database (MICAD). This new database catalogs imaging probe information, describing the specificities, activities, and applications of imaging probes for a wide range of diseases and biological functions.
  2. Imaging Probe Development Center (IPDC). This center offers the production of known imaging probes for the research community in cases where there is no viable commercial supplier, and generates novel imaging probes for biomedical research and clinical applications.

For more information on the Molecular Libraries portion of the Molecular Libraries and Imaging initiatives, contact Geoff Spencer, Communications Specialist, National Human Genome Research Institute, (301) 402-0911,; or Kate Egan, Chief, Science Writing, Press and Dissemination Branch, Office of Science Policy, Planning and Communications, National Institute of Mental Health, 301-443-4536, For more information on the Molecular Imaging portion of the Molecular Libraries and Imaging initiatives, contact Alan McLaughlin, Ph.D., National Institute of Biomedical Imaging and Bioengineering, (301) 451-4780,

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This page last reviewed: October 24, 2008