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Chemical biology is a scientific discipline spanning the fields of chemistry and biology that involves the application of chemical techniques and tools, often compounds produced through synthetic chemistry, to the study and manipulation of biological systems. This is a subtle difference from biochemistry, which is classically defined as the study of the chemistry of biomolecules. For example, a biochemist would seek to understand the three-dimensional structure of a protein and how that structure relates to the chemistry of the protein. Chemical biologists attempt to utilize chemical principles to modulate systems to either investigate the underlying biology or create new function. In this way, the research done by chemical biologists is often closer related to that of cell biology than biochemistry. In short, biochemists deal with the chemistry of biology, chemical biologists deal with chemistry applied to biology.

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 biology 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

host-guest chemistry), bioorganic chemistry, pharmacology, genetics, biochemistry, and metabolic engineering
.

Systems of interest

Proteomics

Main article: Proteomics

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

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 involving kinase and phosphatase signaling. In this regard, Kevan Shokat at UCSF has developed a method for selectively inhibiting a given kinase upon the addition of an otherwise biologically orthogonal competitive inhibitor (1-napthylmethyl-PP1)[1]. Shokat's technique involves altering a protein kinase (by mutating the so-called "gatekeeper" residue in the kinase catalytic domain) to contain an unnatural hydrophobic binding pocket which distinguishes it from the other highly homologous cellular kinases, allowing it to be selectively inhibited. A related method has been developed in his lab which uses these so-called "analog-sensitive" kinases to label their substrates using an unnatural ATP (adenosine triphosphate) 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,

the Scripps Research Institute
has evolved bacteria to install synthetic, non-natural amino acids into proteins.

Glycobiology

While

Carolyn Bertozzi at University of California, 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. These approaches are identical to those employed in the discipline of Pharmacology.

Molecular Sensing

Chemical biologists are also interested in developing new small-molecule and biomolecule-based tools to study biological processes, often by molecular imaging techniques

Roger Tsien's work developing calcium-sensing fluorescent compounds as well as pioneering the use of GFP, for which he was awarded the 2008 Nobel Prize in Chemistry[3]
. Today, researchers continue to utilize basic chemical principles to develop new compounds for the study of biological metabolites and processes.

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 vitro to produce new catalytic function.

Protein Misfolding and Aggregation as a Cause of Disease

Through the

amino acids. The resulting polypeptides fold into more complex secondary, tertiary, and quaternary structures to form proteins. Based on both the sequence and the structure, a particular protein is conferred its cellular function. However, sometimes the folding process fails due to mutations in either the genetic code or the amino acid sequence or due to changes in the cell environment (e.g. pH, temperature, reduction potential, etc.). Misfolding occurs more often in aged individuals or in cells exposed to a high degree of oxidative stress
, but a fraction of all proteins misfold at some point even in the healthiest of cells.

Normally when a protein does not fold correctly,

Alzheimer’s disease
, in which the protein begins to aggregate causing it to become insoluble and non-functional.

A common form of aggregation is long, ordered spindles called amyloid fibrils which are implicated in Alzheimer’s disease which have been shown to consist of cross-linked

Creutzfeldt-Jakob disease and bovine spongiform encephalopathy. In both structures, aggregation occurs through hydrophobic interactions and water must be excluded from the binding surface before aggregation can occur[5]. A movie of this process can be seen in "Chemical and Engineering News"[6]
. The diseases associated with misfolded proteins are life-threatening and extremely debilitating which makes them an important target for chemical biology research.

Protein misfolding has previously been studied using both computational approaches as well as in vivo biological assays in

model organisms such as Drosophila melanogaster and C. elegans. Computational models use a de novo process to calculate possible protein structures based on input parameters such as amino acid sequence, solvent effects, and mutations. This method has the shortcoming that the cell environment has been drastically simplified which limits the factors that influence folding and stability. On the other hand, biological assays can be quite complicated to perform in vivo with high-throughput
like efficiency and there always remains the question of how well lower organism systems approximate human systems.

Dobson et al. propose combining these two approaches such that computational models based on the organism studies can begin to predict what factors will lead to protein misfolding[7]. Several experiments have already been performed based on this strategy. In experiments on Drosophila, different mutations of beta amyloid peptides were evaluated based on the survival rates of the flies as well as their motile ability. The findings from the study show that the more a protein aggregates, the more detrimental the neurological dysfunction [7][8][9]. Further studies using tranthyretin, a component of cerebrospinal fluid which binds to beta amyloid peptide deterring aggregation but can itself aggregate especially when mutated, indicate that aggregation prone proteins may not aggregate where they are secreted and rather are deposited in specific organs or tissues based on each mutation[10]. Kelly et al. have shown that the more stable, both kinetically and thermodynamically, a misfolded protein is the more likely the cell is to secrete it from the endoplasmic reticulum rather than targeting the protein for degradation.[11] Additionally, the more stress that a cell feels from misfolded proteins, the more probable new proteins will misfold[12]. These experiments as well as others having begun to elucidate both the intrinsic and extrinsic causes of misfolding as well as how the cell recognizes if proteins have folded correctly.

As more information is obtained on how the cell copes with misfolded proteins, new therapeutic strategies begin to emerge. An obvious path would be prevention of misfolding. However, if protein misfolding cannot be avoided, perhaps the cell’s natural mechanisms for degradation can be bolstered to better deal with the proteins before they begin to aggregate[13]. Before these ideas can be realized, many more experiments need to be done to understand the folding and degradation machinery as well as what factors lead to misfolding. More information about protein misfolding and how it relates to disease can be found in the recently published book by Dobson, Kelly, and Rameriz-Alvarado entitled Protein Misfolding Diseases Current and Emerging Principles and Therapies[14].

Protein Design by Directed Evolution

One of the primary goals of

proteins with a desired structure and chemical activity. Because our knowledge of the relationship between primary sequence, structure, and function of proteins is limited, rational design of new proteins with enzymatic activity is extremely challenging. Directed evolution, repeated cycles of genetic diversification followed by a screening or selection process, can be used to mimic Darwinian evolution in the laboratory to design new proteins with a desired activity.[15]

Several methods exist for creating large libraries of sequence variants. Among the most widely used are subjecting

fluorescence-activated cell sorting (FACS),[18] mRNA display,[19] phage display, or in vitro compartmentalization.[20]
Once useful variants are found, their DNA sequence is amplified and subjected to further rounds of diversification and selection. Since only proteins with the desired activity are selected, multiple rounds of directed evolution lead to proteins with an accumulation beneficial traits.

There are two general strategies for choosing the starting sequence for a directed evolution experiment: de novo design and redesign. In a protein design experiment, an initial sequence is chosen at random and subjected to multiple rounds of directed evolution. This has been employed successfully to create a family of ATP-binding proteins with a new folding pattern not found in nature.[21] Random sequences can also be biased towards specific folds by specifying the characteristics (such as polar vs. nonpolar) but not specific identity of each amino acid in a sequence. Among other things, this strategy has been used to successfully design four-helix bundle proteins [22][23]. Because it is often thought that a well-defined structure is required for activity, biasing a designed protein towards adopting a specific folded structure is likely to increase the frequency of desirable variants in constructed libraries.

In a protein redesign experiment, an existing sequence serves as the starting point for directed evolution. In this way, old proteins can be redesigned for increased activity or new functions. Protein redesign has been used for protein simplification, creation of new quaternary structures, and topological redesign of a

sesquiterpenes, to create enzymes that selectively synthesize individual products.[28] Similarly, completely new functions can be selected for from existing protein scaffolds. In one example of this, an RNA ligase was created from a zinc finger scaffold after 17 rounds of directed evolution. This new enzyme catalyzes a chemical reaction not known to be catalyzed by any natural enzyme.[29]

Computational methods, when combined with experimental approaches, can significantly assist both the design and redesign of new proteins through directed evolution. Computation has been used to design proteins with unnatural folds, such as a right-handed coiled coil.[30] These computational approaches could also be used to redesign proteins to selectively bind specific target molecules. By identifying lead sequences using computational methods, the occurrence of functional proteins in libraries can be dramatically increased before any directed evolution experiments in the laboratory.


Publications

  • ACS Chemical Biology - The new Chemical Biology journal from the American Chemical Society.
  • Bioorganic & Medicinal Chemistry - The Tetrahedron Journal for Research at the Interface of Chemistry and Biology
  • ChemBioChem – A European Journal of Chemical Biology
  • Chemical Biology
    - A point of access to chemical biology news and research from across RSC Publishing
  • Chemistry & Biology - An interdisciplinary journal that publishes papers of exceptional interest in all areas at the interface between chemistry and biology.
  • Journal of Chemical Biology - A new journal publishing novel work and reviews at the interface between biology and the physical sciences, published by Springer.
  • Journal of the Royal Society Interface - A cross-disciplinary publication promoting research at the interface between the physical and life sciences
  • Molecular BioSystems
    - Chemical biology journal with a particular focus on the interface between chemistry and the -omic sciences and systems biology.
  • 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.
  • Wiley Encyclopedia of Chemical Biology

References

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