User:Bread6/Chemical Biology

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Chemical biology is a scientific discipline between the fields of chemistry and biology. The discipline involves the application of chemical techniques, analysis, and often small molecules produced through synthetic chemistry, to the study and manipulation of biological systems. Although often confused with biochemistry, which studies the chemistry of biomolecules and regulation of biochemical pathways within and between cells, chemical biology remains distinct by focusing on the 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 into chemical biology has led to the creation of multiple 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.

Undergraduate Education
Despite an increase in biological research within chemistry departments, attempts at integrating chemical biology into undergraduate curricula are lacking. For example, although the American Chemical Society (ACS) requires for foundational courses in a Chemistry Bachelor's degree to include biochemistry, no other biology-related chemistry course is required.

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.

Glycobiology
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
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.

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. Unfortunately, these requirements are often hard 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. Unfortunately, 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, cyclooctyne reacts with azido-molecules with distinctive vigor.

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.