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Chemical biology is a scientific field at the interface of chemistry and biology that applies chemical methods to the study of biological systems. It involves the use of chemical techniques, analytical approaches, and often produced through synthetic chemistry to probe, characterize, and manipulate biological processes and systems at the molecular level.
Although it overlaps with biochemistry, which focuses on the chemistry of biomolecules and the regulation of biochemical pathways within and between cells, chemical biology is distinguished by its emphasis on the deliberate design and application of chemical tools to address biological questions.
Friedrich Wöhler's 1828 synthesis of urea is an early example of the application of synthetic chemistry to advance biology. It showed that biological compounds could be synthesized with inorganic starting materials and weakened the previous notion of vitalism, or that a 'living' source was required to produce organic compounds. Wöhler's work is often considered to be instrumental in the development of organic chemistry and natural product synthesis, both of which play a large part in modern chemical biology.
Friedrich Miescher's work during the late 19th century investigating the cellular contents of human leukocytes led to the discovery of 'nuclein', which would later be renamed DNA. After isolating the nuclein from the nucleus of leukocytes through protease digestion, Miescher used chemical techniques such as elemental analysis and solubility tests to determine the composition of nuclein. This work would lay the foundations for Watson and Crick's discovery of the double-helix structure of DNA.
The rising interest in chemical biology has led to several journals dedicated to the field. Nature Chemical Biology, created in 2005, and ACS Chemical Biology, created in 2006, are two of the most well-known journals in this field, with impact factors of 14.8 and 4.0 respectively.
| +List of Nobel laureates in chemical biology !Laureate !Year !Discipline !Contribution | |||
| Paul Berg | 1980 | Chemistry | Recombinant DNA |
| Walter Gilbert Frederick Sanger | 1980 | Chemistry | Genome sequencing |
| Kary Mullis | 1993 | Chemistry | Polymerase chain reaction |
| Michael Smith | 1993 | Chemistry | Site-directed mutagenesis |
| Venkatraman Ramakrishnan Thomas A. Steitz Ada Yonath | 2009 | Chemistry | Elucidation of ribosome structure and function |
| Robert Lefkowitz Brian Kobilka | 2012 | Chemistry | G-protein-coupled receptors |
| Frances Arnold George P. Smith Gregory Winter | 2018 | Chemistry | Enzyme development through directed evolution |
| Emmanuelle Charpentier Jennifer Doudna | 2020 | Chemistry | CRISPR/Cas9 genetic scissors |
| Barry Sharpless Morten Meldal | 2022 | Chemistry | Click chemistry |
| Carolyn Bertozzi | 2022 | Chemistry | Applications of click chemistry in living organisms |
| Demis Hassabis John M. Jumper | 2024 | Chemistry | AlphaFold |
To make protein-sized polypeptide chains with the small peptide fragments made by synthesis, chemical biologists can use the process of native chemical ligation. Native chemical ligation involves the coupling of a C-terminal thioester and an N-terminal cysteine residue, ultimately resulting in formation of a "native" amide bond. (2013). 9780123822390, Academic Press. ISBN 9780123822390 Other strategies that have been used for the ligation of peptide fragments using the acyl transfer chemistry first introduced with native chemical ligation include expressed protein ligation, sulfurization/desulfurization techniques, and use of removable thiol auxiliaries.
Several methods exist for creating large libraries of sequence variants. Among the most widely used are subjecting DNA to UV radiation or mutagen, error-prone PCR, genetic code, or recombination. 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 FACS, mRNA display, phage display, and in vitro compartmentalization. Once useful variants are found, their DNA sequence is amplified and subjected to further rounds of diversification and selection.
The development of directed evolution methods was honored in 2018 with the awarding of the Nobel Prize in Chemistry to Frances Arnold for evolution of enzymes, and George Smith and Gregory Winter for phage display.
The coupling of a probe to a molecule of interest must occur within a reasonably short time frame; therefore, the kinetics of the coupling reaction should be highly favorable. Click chemistry is well suited to fill this niche, since click reactions are rapid, spontaneous, selective, and high-yielding. However, the most famous "click reaction," a 3+2 cycloaddition between an azide and an acyclic alkyne, is copper-catalyzed, posing a serious problem for use in vivo due to copper's toxicity. To bypass the necessity for a catalyst, Carolyn R. Bertozzi's lab introduced inherent strain into the alkyne species by using a cyclic alkyne. In particular, Cycloalkyne reacts with azido-molecules with distinctive vigor.
Functional or homology screening strategies have been used to identify genes that produce small bioactive molecules. Functional metagenomic studies are designed to search for specific phenotypes that are associated with molecules with specific characteristics. Homology metagenomic studies, on the other hand, are designed to examine genes to identify conserved sequences that are previously associated with the expression of biologically active molecules.
Functional metagenomic studies enable the discovery of novel genes that encode biologically active molecules. These assays include top agar overlay assays where antibiotics generate zones of growth inhibition against test microbes, and pH assays that can screen for pH change due to newly synthesized molecules using pH indicator on an agar plate. Substrate-induced gene expression screening (SIGEX), a method to screen for the expression of genes that are induced by chemical compounds, has also been used to search for genes with specific functions. Homology-based metagenomic studies have led to a fast discovery of genes that have homologous sequences as the previously known genes that are responsible for the biosynthesis of biologically active molecules. As soon as the genes are sequenced, scientists can compare thousands of bacterial genomes simultaneously. The advantage over functional metagenomic assays is that homology metagenomic studies do not require a host organism system to express the metagenomes, thus this method can potentially save the time spent on analyzing nonfunctional genomes. These also led to the discovery of several novel proteins and small molecules. In addition, an in silico examination from the Global Ocean Metagenomic Survey found 20 new lantibiotic cyclases.
Through the use of small molecule modulators of protein kinases, chemical biologists have gained a better understanding of the effects of protein phosphorylation. For example, nonselective and selective kinase inhibitors, such as a class of pyridinylimidazole compounds are potent inhibitors useful in the dissection of MAP kinase signaling pathways. These pyridinylimidazole compounds function by targeting the ATP binding pocket. Although this approach, as well as related approaches, with slight modifications, has proven effective in a number of cases, these compounds lack adequate specificity for more general applications. Another class of compounds, mechanism-based inhibitors, combines knowledge of the kinase enzymology with previously utilized inhibition motifs. For example, a "bisubstrate analog" inhibits kinase action by binding both the conserved ATP binding pocket and a protein/peptide recognition site on the specific kinase. Research groups also utilized ATP analogs as chemical probes to study kinases and identify their substrates. (2026). 9783527683031, Wiley. ISBN 9783527683031
The development of novel chemical means of incorporating phosphomimetics amino acids into proteins has provided important insight into the effects of phosphorylation events. Phosphorylation events have typically been studied by mutating an identified phosphorylation site (serine, threonine or tyrosine) to an amino acid, such as alanine, that cannot be phosphorylated. However, these techniques come with limitations and chemical biologists have developed improved ways of investigating protein phosphorylation. By installing phospho-serine, phospho-threonine or analogous phosphonate mimics into native proteins, researchers are able to perform in vivo studies to investigate the effects of phosphorylation by extending the amount of time a phosphorylation event occurs while minimizing the often-unfavorable effects of mutations. Expressed protein ligation, has proven to be successful techniques for synthetically producing proteins that contain phosphomimetic molecules at either terminus. In addition, researchers have used unnatural amino acid mutagenesis at targeted sites within a peptide sequence.
Advances in chemical biology have also improved upon classical techniques of imaging kinase action. For example, the development of peptide biosensors—peptides containing incorporated improved temporal resolution of in vitro binding assays. One of the most useful techniques to study kinase action is Fluorescence Resonance Energy Transfer (FRET). To utilize FRET for phosphorylation studies, fluorescent proteins are coupled to both a phosphoamino acid binding domain and a peptide that can be phosphorylated. Upon phosphorylation or dephosphorylation of a substrate peptide, a conformational change occurs that results in a change in fluorescence. FRET has also been used in tandem with Fluorescence Lifetime Imaging Microscopy (FLIM) or fluorescently conjugated antibodies and flow cytometry to provide quantitative results with excellent temporal and spatial resolution.
Fluorescent techniques have been used to assess a number of protein dynamics including protein tracking, conformational changes, protein–protein interactions, protein synthesis and turnover, and enzyme activity, among others. Three general approaches for measuring protein net redistribution and diffusion are single-particle tracking, correlation spectroscopy and photomarking methods. In single-particle tracking, the individual molecule must be both bright and sparse enough to be tracked from one video to the other. Correlation spectroscopy analyzes the intensity fluctuations resulting from migration of fluorescent objects into and out of a small volume at the focus of a laser. In photomarking, a fluorescent protein can be dequenched in a subcellular area with the use of intense local illumination and the fate of the marked molecule can be imaged directly. Michalet and coworkers used quantum dots for single-particle tracking using biotin-quantum dots in HeLa cells. One of the best ways to detect conformational changes in proteins is to label the protein of interest with two fluorophores within close proximity. FRET will respond to internal conformational changes result from reorientation of one fluorophore with respect to the other. One can also use fluorescence to visualize enzyme activity, typically by using a quenched activity-based proteomics (qABP). Covalent binding of a qABP to the active site of the targeted enzyme will provide direct evidence concerning if the enzyme is responsible for the signal upon release of the quencher and regain of fluorescence.
Although a chemical biology course is often not required for an undergraduate degree in Chemistry, many universities now provide introductory chemical biology courses for their undergraduate students. The University of British Columbia, for example, offers a fourth-year course in synthetic chemical biology.
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