Chemical biology
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 small molecules 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.
History
Although considered a relatively new scientific field, the term "chemical biology" has been in use since the early 20th century, and has roots in scientific discovery from the early 19th century. The term 'chemical biology' can be traced back to an early appearance in a book published by Alonzo E. Taylor in 1907 titled "On Fermentation", and was subsequently used in John B. Leathes' 1930 article titled "The Harveian Oration on The Birth of Chemical Biology". However, it is unclear when the term was first used.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.
Nobel laureates in chemical biology
Research areas
Glycobiology
is the study of the structure and function of carbohydrates. While DNA, RNA, and proteins are encoded at the genetic level, carbohydrates are not encoded directly from the genome, and thus require different tools for their study. By applying chemical principles to glycobiology, novel methods for analyzing and synthesizing carbohydrates can be developed. For example, cells can be supplied with synthetic variants of natural sugars to probe their function. Carolyn Bertozzi's research group has developed methods for site-specifically reacting molecules at the surface of cells via synthetic sugars.Combinatorial chemistry
involves simultaneously synthesizing a large number of related compounds for high-throughput analysis. Chemical biologists are able to use principles from combinatorial chemistry in synthesizing active drug compounds and maximizing screening efficiency. Similarly, these principles can be used in areas of agriculture and food research, specifically in the syntheses of unnatural products and in generating novel enzyme inhibitors.Peptide synthesis
Chemical synthesis of proteins is a valuable tool in chemical biology as it allows for the introduction of non-natural amino acids as well as residue-specific incorporation of "posttranslational modifications" such as phosphorylation, glycosylation, acetylation, and even ubiquitination. These properties are valuable for chemical biologists as non-natural amino acids can be used to probe and alter the functionality of proteins, while post-translational modifications are widely known to regulate the structure and activity of proteins. Although strictly biological techniques have been developed to achieve these ends, the chemical synthesis of peptides often has a lower technical and practical barrier to obtaining small amounts of the desired protein.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. 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.
Enrichment techniques for proteomics
Chemical biologists work to improve proteomics through the development of enrichment strategies, chemical affinity tags, and new probes. Samples for proteomics often contain many peptide sequences and the sequence of interest may be highly represented or of low abundance, which creates a barrier for their detection. Chemical biology methods can reduce sample complexity by selective enrichment using affinity chromatography. This involves targeting a peptide with a distinguishing feature like a biotin label or a post translational modification. Methods have been developed that include the use of antibodies, lectins to capture glycoproteins, and immobilized metal ions to capture phosphorylated peptides and enzyme substrates to capture select enzymes.Enzyme probes
To investigate enzymatic activity as opposed to total protein, activity-based reagents have been developed to label the enzymatically active form of proteins. For example, serine hydrolase- and cysteine protease-inhibitors have been converted to suicide inhibitors. This strategy enhances the ability to selectively analyze low abundance constituents through direct targeting. Enzyme activity can also be monitored through converted substrate. Identification of enzyme substrates is a problem of significant difficulty in proteomics and is vital to the understanding of signal transduction pathways in cells. A method that has been developed uses "analog-sensitive" kinases to label substrates using an unnatural ATP analog, facilitating visualization and identification through a unique handle.Employing biology
Many research programs are also focused on employing natural biomolecules to perform biological tasks or to support a new chemical method. In this regard, chemical biology 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. Additionally, heterobifunctional synthetic small molecules such as dimerizers or PROTACs bring two proteins together inside cells, which can synthetically induce important new biological functions such as targeted protein degradation.Directed evolution
A primary goal 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 engineered activities is extremely challenging. In directed evolution, repeated cycles of genetic diversification followed by a screening or selection process, can be used to mimic natural selection in the laboratory to design new proteins with a desired activity.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. 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.
Bioorthogonal reactions
Successful labeling of a molecule of interest requires specific functionalization of that molecule to react chemospecifically with an optical probe. For a labeling experiment to be considered robust, that functionalization must minimally perturb the system. These requirements are often difficult to meet. Many of the reactions normally available to organic chemists in the laboratory are unavailable in living systems. Water- and redox- sensitive reactions would not proceed, reagents prone to nucleophilic attack would offer no chemospecificity, and any reactions with large kinetic barriers would not find enough energy in the relatively low-heat environment of a living cell. Thus, chemists have recently developed a panel of bioorthogonal chemistry that proceed chemospecifically, despite the milieu of distracting reactive materials in vivo.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 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, cyclooctyne reacts with azido-molecules with distinctive vigor.