Chemical biology

Encyclopedia : C : CH : CHE : Chemical biology

Chemical biology is a scientific discipline spanning the fields of chemistry and biology that frequently employs compounds produced by synthetic chemistry to study and manipulate biological systems.

Contents

1 Introduction
2 Systems of Interest

2.1 The Proteome
2.2 Glycobiology
2.3 Combinatorial Chemistry
2.4 Employing Biology

3 Research Institutes and Graduate Programs
4 Publications
5 See also

Introduction

Some forms of Chemical Biology attempt to answer biological questions by directly probing living systems at the chemical level. In contrast to research using biochemistry, genetics, or molecular biology, where mutagenesis can provide a new version of the organism or cell of interest, chemical biological studies sometime probe systems in vitro and in vivo with small molecules that have been designed for a specific purpose or identified on the basis of biochemical or cell-based screening.

Chemical biology is one of many interfacial sciences which are symptiomatic of a general trend in the early 21st century away from older, reductionist fields toward those whose goals are to achieve a description of scientific holism.

Chemical biology has historical and philosophical roots in the interfacial sciences of Medicinal chemistry, Supramolecular chemistry (Host-guest chemistry especially), Bioorganic chemistry, Genetics, and Biochemistry. The field has its origins in the 1950s in the work of Linus Pauling at Caltech. More recently, the field has been rejuvenated by the work of chemistry labs including Peter Dervan at Caltech, Peter Schultz then at UC-Berkeley, and Stuart Schreiber at Harvard.

Systems of Interest

The Proteome

After the completion of the human genome project, many scientists realized the next big target would be the human proteome. As genes ultimately encode cellular proteins, the purpose and ultimate destination of proteins in cells is technically encoded as well. However, in practice, the ability to determine the structure, let alone function, of a protein just from its genetic sequence is impossible. Chemical biology is attempting to answer many questions about the function, structure, affinity and location of all the proteins within a living cell.

The global analysis of the proteome is called proteomics. The major challenge in proteomics is that in any given tissue, there are approximately 10,000 different proteins being expressed at levels that vary by as much as six orders of magnitude. Chemical biologist Stuart Schreiber advocates building a “perturbogen” library of small molecules that could specifically activate or deactivate every protein in the human body. Schreiber estimates such a project would require at least a decade. A purpose of the library would be to enable biomedical engineers to develop therapies more efficiently. A number of scientists have developed ways to break the proteome down into meaningful pieces that can be studied more easily. Notably, activity based proteomics developed by Benjamin Cravatt III uses specially designed chemical probes to analyze classes of active enzymes in within a tissue.

Another challenge of chemical biology is to decipher the myriad signal transduction pathways through common tools for kinase and phosphorylase profiling. In this regard, [Kevan Shokat] at [UCSF] has developed a method for "watching" the activity of a single kinase in a living cell upon addition of a small molecule activator. Dr. Shokat's technique, which has humorously been called "the central dogma of chemical biology" (probably due to the frequency with which it is copied by other chemical biologists), involves engineering a protein kinase so that it will "label" its substrates using an unnatural synthetic ATP (Adenosine triphophate) analog, facilitating their visualization and identification. Identification of enzyme substrates (of which there may be hundreds or thousands, many of which are unknown) is a problem of significant difficulty in proteomics and is vital to the understanding of signal transduction pathways in cells; techniques for "labelling" cellular substrates of enzymes are a typical approach used by chemical biologists to address this problem.

Many researchers are working on ways to manipulate the way that proteins are assembled by cellular systems. In this regard, [Peter Schultz] at the Scripps Research Institute has evolved bacteria to install synthetic, non-natural amino acids into proteins.

Glycobiology

While DNA, RNA and proteins are all encoded at the genetic level, there exists a separate system of trafficked molecules in the cell that are not encoded directly at any level: sugars. Thus, Glycobiology is an area of dense research for chemical biologists. Metabolic Engineering is a technique used to submit synthetic sugar molecules to living cells in order to probe the function of those sugars in vivo. [Carolyn Bertozzi] at [UC-Berkeley] has developed a method for site-specifically reacting molecules the surface of cells that have been labeled with synthetic sugars.

Combinatorial Chemistry

Some chemical biologists use automated synthesis of many diverse compounds in order to experiment with effects of small molecules on biological processes. More specifically, they observe changes in the behaviors of proteins when small molecules bind to them. Such experiments may supposedly lead to discovery of small molecules with antibiotic or chemotherapeutic properties. Indeed, some scientists (such as Jon Clardy of the Harvard Medical School) hope chemical biology will lead to cures for malaria, tuberculosis, and AIDS.

Employing Biology

Many research programs are also focused on employing natural biomolecules to perform a task or act as support for a new chemical method or material. In this regard, researchers have shown that DNA can serve as a template for synthetic chemistry, self-assembling proteins can serve as a structural scaffold for new materials, and RNA can be evolved in vivo to produce new catalytic function.

Research Institutes and Graduate Programs

Publications

[ChemBioChem] – A European Journal of Chemical Biology
[ACS Chemical Biology] - The new Chemical Biology journal from the American Chemical Society.
[Nature Chemical Biology] - A monthly multidisciplinary journal providing an international forum for the timely publication of significant new research at the interface between chemistry and biology.
[Bioorganic & Medicinal Chemistry] - The Tetrahedron Journal for Research at the Interface of Chemistry and Biology
[Chemistry & Biology] - An interdisciplinary journal that publishes papers of exceptional interest in all areas at the interface between chemistry and biology.