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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

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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 interfacial sciences that are characteristic of a general trend away from older, reductionist fields toward those whose goals are to achieve a description of scientific holism. In this sense, it is related to other fields such as proteomics. Chemical biology has historical and philosophical roots in medicinal chemistry, supramolecular chemistry (particularly host-guest chemistry), bioorganic chemistry, pharmacology, genetics, biochemistry, and metabolic engineering.

Systems of interest

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Proteomics

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

Glycobiology

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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 direct level: sugars. Thus, glycobiology is an area of dense research for chemical biologists. For instance, live cells can be supplied with synthetic variants of natural sugars in order to probe the function of the sugars in vivo. 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

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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

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Chemical biologists are also interested in developing new small-molecule and biomolecule-based tools to study biological processes, often by molecular imaging techniques[2]. The field of molecular sensing was popularized by 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

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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

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Through the transcription and translation process, DNA encodes for specific sequences of 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, molecular chaperones in the cell can encourage refolding back into its active form. When refolding is not an option, the cell can also target the protein for degradation back into its component amino acids via proteolytic, lysosomal, or autophagic mechanisms. However under certain conditions or with certain mutations, the cells can no longer cope with the misfolded protein(s) and a disease state results. Either the protein has a loss-of-function, such as in cystic fibrosis, in which it loses activity or cannot reach its target, or the protein has a gain-of-function, such as with 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 beta sheet regions perpendicular to the backbone of the polypeptide[4]. Another form of aggregation occurs with prion proteins, the glycoproteins found with 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

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One of the primary goals of protein engineering is the design of novel peptides or 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 DNA to UV radiation or chemical mutagens, error-prone PCR, degenerate codons, or recombination [16][17]. Once a large library of variants is created, selection or screening techniques are used to find mutants with a desired attribute. Common selection/screening techniques include 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 chorismate mutase [24][25][26][27]. To develop enzymes with new activities, one can take advantage of promiscuous enzymes or enzymes with significant side reactions. In this regard, directed evolution has been used on γ-humulene synthase, an enzyme that creates over 50 different 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

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References

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  1. ^ http://www.nature.com/nature/journal/v407/n6802/full/407395a0.html
  2. ^ http://pubs.acs.org/doi/abs/10.1021/cb700248m
  3. ^ http://nobelprize.org/nobel_prizes/chemistry/laureates/2008/index.html
  4. ^ Jordens, S., Adamick, J., Amar-Yuli, I., and Mezzenga, R. (2010) Disassembly and Reassembly of Amyloid Fibrils in Water−Ethanol Mixtures, In Biomacromolecules, ACS Publications. DOI:http://dx.doi.org/10.1021/bm101119t
  5. ^ Reddy, G., Straub, J. E., and Thirumalai, D. (2010) Dry amyloid fibril assembly in a yeast prion peptide is mediated by long-lived structures containing water wires, Proceedings of the National Academy of Sciences of the United States of America 107, 21459-21464. DOI: http://dx.doi.org/10.1073/pnas.1008616107
  6. ^ Borman, S. A. (2010) Water Factors In On Amyloid And Prion Aggregation Rates, In Chemical and Engineering News, ACS Publications
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  8. ^ Luheshi, L. M., Tartaglia, G. G., Brorsson, A.-C., Pawar, A. P., Watson, I. E., Chiti, F., Vendruscolo, M., Lomas, D. A., Dobson, C. M., and Crowther, D. C. (2007) Systematic In Vivo Analysis of the Intrinsic Determinants of Amyloid β Pathogenicity, PLoS Biol 5, e290.DOI: http://dx.doi.org/10.1371/journal.pbio.0050290
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  13. ^ Cohen, E., Bieschke, J., Perciavalle, R. M., Kelly, J. W., and Dillin, A. (2006) Opposing Activities Protect Against Age-Onset Proteotoxicity, Science 313, 1604-1610. DOI: http://dx.doi.org/10.1126/science.1124646
  14. ^ Ramirez-Alvarado, M., Kelly, J. W., and Dobson, C. M., (Eds.) (2010) Protein Misfolding Diseases Current and Emerging Principles and Therapies, John Wiley and Sons, Hoboken
  15. ^ Jackel, C., Kast, P., and Hilvert, D. (2008) Protein design by directed evolution, Ann Rev Biophys 37, 153-173. DOI: http://dx.doi.org/10.1146/annurev.biophys.37.032807.125832
  16. ^ Jackel, C., Kast, P., and Hilvert, D. (2008) Protein design by directed evolution, Ann Rev Biophys 37, 153-173. DOI: http://dx.doi.org/10.1146/annurev.biophys.37.032807.125832
  17. ^ Bittker, J. A., Le, B. V., Liu, J. M., and Liu, D. R. (2004) Directed evolution of protein enzymes using nonhomologous random recombination, P Natl Acad Sci USA 101, 7011-7016. DOI: http://dx.doi.org/10.1073/pnas.0402202101
  18. ^ Aharoni, A., Griffiths, A. D., and Tawfik, D. S. (2005) High-throughput screens and selections of enzyme-encoding genes, Curr Opin Chem Biol 9, 210-216. DOI: http://dx.doi.org/10.1016/j.cbpa.2005.02.002
  19. ^ Wilson, D. S., Keefe, A. D., and Szostak, J. W. (2001) The use of mRNA display to select high-affinity protein-binding peptides, P Natl Acad Sci USA 98, 3750-3755. DOI: http://dx.doi.org/10.1073/pnas.061028198
  20. ^ Tawfik, D. S., and Griffiths, A. D. (1998) Man-made cell-like compartments for molecular evolution, Nat Biotechnol 16, 652-656. DOI: http://dx.doi.org/10.1038/nbt0798-652
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  24. ^ Bittker, J. A., Le, B. V., Liu, J. M., and Liu, D. R. (2004) Directed evolution of protein enzymes using nonhomologous random recombination, P Natl Acad Sci USA 101, 7011-7016. DOI: http://dx.doi.org/10.1073/pnas.0402202101
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  28. ^ Yoshikuni, Y., Ferrin, T. E., and Keasling, J. D. (2006) Designed divergent evolution of enzyme function, Nature 440, 1078-1082. DOI: http://dx.doi.org/10.1038/nature04607
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