Chemical biology

Although considered a relatively new scientific field,{{Cite book | vauthors = Miller A, Tanner J |title=Essentials of Chemical Biology: Structure and Dynamics of Biological Macromolecules |publisher=John Wiley & Sons, Ltd |year=2008 |isbn=978-0-470-84530-1 |location=England |pages=vi - x |language=English}} the term "chemical biology" has been in use since the early 20th century,{{cite journal | vauthors = Hricovini M, Jampilek J | title = Chemistry towards Biology | journal = International Journal of Molecular Sciences | volume = 24 | issue = 4 | pages = 3998 | date = February 2023 | pmid = 36835407 | pmc = 9960482 | doi = 10.3390/ijms24043998 | doi-access = free }} 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",{{Cite book | vauthors = Taylor AE |title=On fermentation |publisher=University Press |year=1907 |series=8 |volume=1}} and was subsequently used in John B. Leathes' 1930 article titled "The Harveian Oration on The Birth of Chemical Biology".{{cite journal | vauthors = Leathes JB | title = The Harveian Oration on THE BIRTH OF CHEMICAL BIOLOGY | journal = British Medical Journal | volume = 2 | issue = 3642 | pages = 671–676 | date = October 1930 | pmid = 20775787 | pmc = 2451377 | doi = 10.1136/bmj.2.3642.671 }} 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.{{cite journal | vauthors = Morrison KL, Weiss GA | title = The origins of chemical biology | journal = Nature Chemical Biology | volume = 2 | issue = 1 | pages = 3–6 | date = January 2006 | pmid = 16408079 | doi = 10.1038/nchembio0106-3 | s2cid = 8427286 }} 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.{{cite journal | vauthors = Ramberg PJ | title = The death of vitalism and the birth of organic chemistry: Wohler's urea synthesis and the disciplinary identity of organic chemistry | journal = Ambix | volume = 47 | issue = 3 | pages = 170–195 | date = November 2000 | pmid = 11640223 | doi = 10.1179/amb.2000.47.3.170 | s2cid = 44613876 }}{{cite journal | vauthors = Kinne-Saffran E, Kinne RK | title = Vitalism and synthesis of urea. From Friedrich Wöhler to Hans A. Krebs | journal = American Journal of Nephrology | volume = 19 | issue = 2 | pages = 290–4 | date = 1999 | pmid = 10213830 | doi = 10.1159/000013463 | s2cid = 71727190 }} 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.{{cite journal | vauthors = Hong J | title = Natural product synthesis at the interface of chemistry and biology | journal = Chemistry: A European Journal | volume = 20 | issue = 33 | pages = 10204–10212 | date = August 2014 | pmid = 25043880 | pmc = 4167019 | doi = 10.1002/chem.201402804 }}

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.{{cite journal | vauthors = Dahm R | title = Discovering DNA: Friedrich Miescher and the early years of nucleic acid research | journal = Human Genetics | volume = 122 | issue = 6 | pages = 565–581 | date = January 2008 | pmid = 17901982 | doi = 10.1007/s00439-007-0433-0 | s2cid = 915930 }} This work would lay the foundations for Watson and Crick's discovery of the double-helix structure of DNA.{{cite journal | vauthors = Dahm R | title = Friedrich Miescher and the discovery of DNA | journal = Developmental Biology | volume = 278 | issue = 2 | pages = 274–288 | date = February 2005 | pmid = 15680349 | doi = 10.1016/j.ydbio.2004.11.028 }}

The rising interest in chemical biology has led to several journals dedicated to the field. Nature Chemical Biology, created in 2005,{{Cite web |title=LC Catalog - Item Information (Full Record) |url=https://catalog.loc.gov/vwebv/holdingsInfo?searchId=138775&recCount=25&recPointer=1&bibId=20133862 |access-date=2023-11-06 |website=catalog.loc.gov |language=en}} and ACS Chemical Biology, created in 2006,{{Cite web |title=LC Catalog - Item Information (Full Record) |url=https://catalog.loc.gov/vwebv/holdingsInfo?searchId=138782&recCount=25&recPointer=0&bibId=13889388 |access-date=2023-11-06 |website=catalog.loc.gov | oclc=58045378 |language=en}} are two of the most well-known journals in this field, with impact factors of 14.8{{Cite web |title=Journal Metrics {{!}} Nature Chemical Biology |url=https://www.nature.com/nchembio/journal-impact |access-date=2023-11-06 |website=www.nature.com |language=en}} and 4.0{{Cite web |title=About the Journal |url=https://pubs.acs.org/page/acbcct/about.html |access-date=November 5, 2023 |website=ACS Publications}} respectively.   

File:Sialic_acid_created_with_Chemdraw.png, a commonly studied molecule in glycobiology.]]

Glycobiology is the study of the structure and function of carbohydrates.{{cite journal | vauthors = Dwek RA | title = Glycobiology: Toward Understanding the Function of Sugars | journal = Chemical Reviews | volume = 96 | issue = 2 | pages = 683–720 | date = March 1996 | pmid = 11848770 | doi = 10.1021/cr940283b }} 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.{{cite journal | vauthors = Springer SA, Gagneux P | title = Glycomics: revealing the dynamic ecology and evolution of sugar molecules | journal = Journal of Proteomics | volume = 135 | pages = 90–100 | date = March 2016 | pmid = 26626628 | pmc = 4762723 | doi = 10.1016/j.jprot.2015.11.022 }} By applying chemical principles to glycobiology, novel methods for analyzing and synthesizing carbohydrates can be developed.{{cite journal | vauthors = Wu CY, Wong CH | title = Chemistry and glycobiology | journal = Chemical Communications | volume = 47 | issue = 22 | pages = 6201–6207 | date = June 2011 | pmid = 21503322 | doi = 10.1039/c0cc04359a }} 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.{{Cite web |title=Bertozzi Group |url=https://bertozzigroup.stanford.edu/ |access-date=2023-12-04 |website=Bertozzi Group |language=en-US}}

File:Receptor_Selection_by_Dynamic_Combinatorial_Library.png

Combinatorial chemistry involves simultaneously synthesizing a large number of related compounds for high-throughput analysis.{{cite journal | vauthors = Liu R, Li X, Lam KS | title = Combinatorial chemistry in drug discovery | journal = Current Opinion in Chemical Biology | volume = 38 | pages = 117–126 | date = June 2017 | pmid = 28494316 | pmc = 5645069 | doi = 10.1016/j.cbpa.2017.03.017 }} Chemical biologists are able to use principles from combinatorial chemistry in synthesizing active drug compounds and maximizing screening efficiency.{{cite journal | vauthors = Kennedy JP, Williams L, Bridges TM, Daniels RN, Weaver D, Lindsley CW | title = Application of combinatorial chemistry science on modern drug discovery | journal = Journal of Combinatorial Chemistry | volume = 10 | issue = 3 | pages = 345–354 | date = 2008-05-01 | pmid = 18220367 | doi = 10.1021/cc700187t }} 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.{{cite journal | vauthors = Wong D, Robertson G | title = Applying combinatorial chemistry and biology to food research | journal = Journal of Agricultural and Food Chemistry | volume = 52 | issue = 24 | pages = 7187–7198 | date = December 2004 | pmid = 15563194 | doi = 10.1021/jf040140i | bibcode = 2004JAFC...52.7187W }}

File:Solid_Phase_Peptide_Synthesis.jpg.]]

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.{{cite journal | vauthors = Ramazi S, Zahiri J | title = Posttranslational modifications in proteins: resources, tools and prediction methods | journal = Database | volume = 2021 | date = April 2021 | pmid = 33826699 | pmc = 8040245 | doi = 10.1093/database/baab012 }} 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.{{cite journal | vauthors = Adhikari A, Bhattarai BR, Aryal A, Thapa N, Kc P, Adhikari A, Maharjan S, Chanda PB, Regmi BP, Parajuli N | display-authors = 6 | title = Reprogramming natural proteins using unnatural amino acids | journal = RSC Advances | volume = 11 | issue = 60 | pages = 38126–38145 | date = November 2021 | pmid = 35498070 | pmc = 9044140 | doi = 10.1039/D1RA07028B | bibcode = 2021RSCAd..1138126A }} 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.{{cite journal | vauthors = Chandrudu S, Simerska P, Toth I | title = Chemical methods for peptide and protein production | journal = Molecules | volume = 18 | issue = 4 | pages = 4373–4388 | date = April 2013 | pmid = 23584057 | pmc = 6270108 | doi = 10.3390/molecules18044373 | doi-access = free }}

To make protein-sized polypeptide chains with the small peptide fragments made by synthesis, chemical biologists can use the process of native chemical ligation.{{cite journal | vauthors = Cistrone PA, Bird MJ, Flood DT, Silvestri AP, Hintzen JC, Thompson DA, Dawson PE | title = Native Chemical Ligation of Peptides and Proteins | journal = Current Protocols in Chemical Biology | volume = 11 | issue = 1 | pages = e61 | date = March 2019 | pmid = 30645048 | pmc = 6384150 | doi = 10.1002/cpch.61 }} 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.{{cite book | vauthors = Hermanson GT | chapter = Chapter 3 - The Reactions of Bioconjugation |date= January 2013 | title = Bioconjugate Techniques | edition = Third |pages=229–258 | veditors = Hermanson GT |place=Boston |publisher=Academic Press |doi=10.1016/b978-0-12-382239-0.00003-0 |isbn=978-0-12-382239-0}} 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,{{cite journal | vauthors = Muir TW, Sondhi D, Cole PA | title = Expressed protein ligation: a general method for protein engineering | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 95 | issue = 12 | pages = 6705–6710 | date = June 1998 | pmid = 9618476 | pmc = 22605 | doi = 10.1073/pnas.95.12.6705 | bibcode = 1998PNAS...95.6705M | doi-access = free }} sulfurization/desulfurization techniques,{{cite journal | vauthors = Jin K, Li T, Chow HY, Liu H, Li X | title = P-B Desulfurization: An Enabling Method for Protein Chemical Synthesis and Site-Specific Deuteration | journal = Angewandte Chemie | volume = 56 | issue = 46 | pages = 14607–14611 | date = November 2017 | pmid = 28971554 | doi = 10.1002/anie.201709097 }} and use of removable thiol auxiliaries.{{cite journal | vauthors = Nilsson BL, Soellner MB, Raines RT | title = Chemical synthesis of proteins | journal = Annual Review of Biophysics and Biomolecular Structure | volume = 34 | issue = 1 | pages = 91–118 | date = 2005-06-01 | pmid = 15869385 | pmc = 2845543 | doi = 10.1146/annurev.biophys.34.040204.144700 }}

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.{{cite journal | vauthors = Zhao Y, Jensen ON | title = Modification-specific proteomics: strategies for characterization of post-translational modifications using enrichment techniques | journal = Proteomics | volume = 9 | issue = 20 | pages = 4632–4641 | date = October 2009 | pmid = 19743430 | pmc = 2892724 | doi = 10.1002/pmic.200900398 }} 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.

To investigate enzymatic activity as opposed to total protein, activity-based reagents have been developed to label the enzymatically active form of proteins (see Activity-based proteomics). For example, serine hydrolase- and cysteine protease-inhibitors have been converted to suicide inhibitors.{{cite journal | vauthors = López-Otín C, Overall CM | title = Protease degradomics: a new challenge for proteomics | journal = Nature Reviews. Molecular Cell Biology | volume = 3 | issue = 7 | pages = 509–519 | date = July 2002 | pmid = 12094217 | doi = 10.1038/nrm858 | s2cid = 7586786 }} This strategy enhances the ability to selectively analyze low abundance constituents through direct targeting.{{cite journal | vauthors = Adam GC, Cravatt BF, Sorensen EJ | title = Profiling the specific reactivity of the proteome with non-directed activity-based probes | journal = Chemistry & Biology | volume = 8 | issue = 1 | pages = 81–95 | date = January 2001 | pmid = 11182321 | doi = 10.1016/S1074-5521(00)90060-7 | doi-access = free }} Enzyme activity can also be monitored through converted substrate.{{cite journal | vauthors = Turecek F | title = Mass spectrometry in coupling with affinity capture-release and isotope-coded affinity tags for quantitative protein analysis | journal = Journal of Mass Spectrometry | volume = 37 | issue = 1 | pages = 1–14 | date = January 2002 | pmid = 11813306 | doi = 10.1002/jms.275 | bibcode = 2002JMSp...37....1T }} 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.{{cite journal | vauthors = Blethrow J, Zhang C, Shokat KM, Weiss EL | title = Design and use of analog-sensitive protein kinases | journal = Current Protocols in Molecular Biology | volume = Chapter 18 | pages = Unit 18.11 | date = May 2004 | pmid = 18265343 | doi = 10.1002/0471142727.mb1811s66 | s2cid = 25869680 }}

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 (two-sided) 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.{{cite journal | vauthors = Cermakova K, Hodges HC | title = Next-Generation Drugs and Probes for Chromatin Biology: From Targeted Protein Degradation to Phase Separation | journal = Molecules | volume = 23 | issue = 8 | pages = 1958 | date = August 2018 | pmid = 30082609 | pmc = 6102721 | doi = 10.3390/molecules23081958 | doi-access = free }}

A primary goal of protein engineering is the design of novel peptides or proteins with a desired structure and chemical activity.{{cite encyclopedia | vauthors = Dhanjal JK, Malik V, Radhakrishnan N, Sigar M, Kumari A, Sundar D |title=Computational Protein Engineering Approaches for Effective Design of New Molecules |date= January 2019 |url=https://www.sciencedirect.com/science/article/pii/B9780128096338201507 | encyclopedia =Encyclopedia of Bioinformatics and Computational Biology |pages=631–643 | veditors = Ranganathan S, Gribskov M, Nakai K, Schönbach C |access-date=2023-12-06 |place=Oxford |publisher=Academic Press |doi=10.1016/b978-0-12-809633-8.20150-7 |isbn=978-0-12-811432-2 |s2cid=196001607 }} 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.{{cite journal | vauthors = Kuhlman B, Bradley P | title = Advances in protein structure prediction and design | journal = Nature Reviews. Molecular Cell Biology | volume = 20 | issue = 11 | pages = 681–697 | date = November 2019 | pmid = 31417196 | pmc = 7032036 | doi = 10.1038/s41580-019-0163-x }} 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.{{cite journal | vauthors = Jäckel C, Kast P, Hilvert D | title = Protein design by directed evolution | journal = Annual Review of Biophysics | volume = 37 | pages = 153–173 | year = 2008 | pmid = 18573077 | doi = 10.1146/annurev.biophys.37.032807.125832 }}

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.{{cite journal | vauthors = Taylor SV, Walter KU, Kast P, Hilvert D | title = Searching sequence space for protein catalysts | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 98 | issue = 19 | pages = 10596–10601 | date = September 2001 | pmid = 11535813 | pmc = 58511 | doi = 10.1073/pnas.191159298 | doi-access = free | bibcode = 2001PNAS...9810596T }}{{cite journal | vauthors = Bittker JA, Le BV, Liu JM, Liu DR | title = Directed evolution of protein enzymes using nonhomologous random recombination | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 101 | issue = 18 | pages = 7011–7016 | date = May 2004 | pmid = 15118093 | pmc = 406457 | doi = 10.1073/pnas.0402202101 | doi-access = free | bibcode = 2004PNAS..101.7011B }} 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,{{cite journal | vauthors = Aharoni A, Griffiths AD, Tawfik DS | title = High-throughput screens and selections of enzyme-encoding genes | journal = Current Opinion in Chemical Biology | volume = 9 | issue = 2 | pages = 210–216 | date = April 2005 | pmid = 15811807 | doi = 10.1016/j.cbpa.2005.02.002 }} mRNA display,{{cite journal | vauthors = Wilson DS, Keefe AD, Szostak JW | title = The use of mRNA display to select high-affinity protein-binding peptides | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 98 | issue = 7 | pages = 3750–3755 | date = March 2001 | pmid = 11274392 | pmc = 31124 | doi = 10.1073/pnas.061028198 | doi-access = free | bibcode = 2001PNAS...98.3750W }} phage display, and in vitro compartmentalization.{{cite journal | vauthors = Tawfik DS, Griffiths AD | title = Man-made cell-like compartments for molecular evolution | journal = Nature Biotechnology | volume = 16 | issue = 7 | pages = 652–656 | date = July 1998 | pmid = 9661199 | doi = 10.1038/nbt0798-652 | s2cid = 25527137 }} 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.{{Cite web|url=https://www.nobelprize.org/prizes/chemistry/2018/summary/|title=The Nobel Prize in Chemistry 2018|website=NobelPrize.org|language=en-US|access-date=2018-10-03}}

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.{{cite journal | vauthors = Jonsson AL, Roberts MA, Kiappes JL, Scott KA | title = Essential chemistry for biochemists | journal = Essays in Biochemistry | volume = 61 | issue = 4 | pages = 401–427 | date = October 2017 | pmid = 28951470 | pmc = 5869253 | doi = 10.1042/EBC20160094 }} 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.{{cite book | vauthors = Alberts B, Johnson A, Lewis J, Raff M, Roberts K, Walter P | chapter = Catalysis and the Use of Energy by Cells |date=2002 | chapter-url = https://www.ncbi.nlm.nih.gov/books/NBK26838/ | title = Molecular Biology of the Cell. | edition = 4th |access-date=2023-12-06 |publisher=Garland Science |language=en }} 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;{{cite journal | vauthors = Chen K, Chen X | title = Design and development of molecular imaging probes | journal = Current Topics in Medicinal Chemistry | date = 2010 | volume = 10 | issue = 12 | pages = 1227–1236 | pmid = 20388106 | pmc = 3632640 | doi = 10.2174/156802610791384225 }} 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.

The advances in modern sequencing technologies in the late 1990s allowed scientists to investigate DNA of communities of organisms in their natural environments ("eDNA"), without culturing individual species in the lab. This metagenomic approach enabled scientists to study a wide selection of organisms that were previously not characterized due in part to an incompetent growth condition. Sources of eDNA include soils, ocean, subsurface, hot springs, hydrothermal vents, polar ice caps, hypersaline habitats, and extreme pH environments.{{cite journal | vauthors = Keller M, Zengler K | title = Tapping into microbial diversity | journal = Nature Reviews. Microbiology | volume = 2 | issue = 2 | pages = 141–150 | date = February 2004 | pmid = 15040261 | doi = 10.1038/nrmicro819 | s2cid = 11512358 }} Of the many applications of metagenomics, researchers such as Jo Handelsman, Jon Clardy, and Robert M. Goodman, explored metagenomic approaches toward the discovery of biologically active molecules such as antibiotics.{{cite journal | vauthors = Handelsman J, Rondon MR, Brady SF, Clardy J, Goodman RM | title = Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products | journal = Chemistry & Biology | volume = 5 | issue = 10 | pages = R245–R249 | date = October 1998 | pmid = 9818143 | doi = 10.1016/S1074-5521(98)90108-9 | doi-access = free }}

File:Overview of metagenomic methods.jpg

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.{{cite journal | vauthors = Banik JJ, Brady SF | title = Recent application of metagenomic approaches toward the discovery of antimicrobials and other bioactive small molecules | journal = Current Opinion in Microbiology | volume = 13 | issue = 5 | pages = 603–609 | date = October 2010 | pmid = 20884282 | pmc = 3111150 | doi = 10.1016/j.mib.2010.08.012 }}

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.{{cite journal | vauthors = Daniel R | title = The metagenomics of soil | journal = Nature Reviews. Microbiology | volume = 3 | issue = 6 | pages = 470–478 | date = June 2005 | pmid = 15931165 | doi = 10.1038/nrmicro1160 | s2cid = 32604394 }} 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.{{cite journal | vauthors = Bunterngsook B, Kanokratana P, Thongaram T, Tanapongpipat S, Uengwetwanit T, Rachdawong S, Vichitsoonthonkul T, Eurwilaichitr L | display-authors = 6 | title = Identification and characterization of lipolytic enzymes from a peat-swamp forest soil metagenome | journal = Bioscience, Biotechnology, and Biochemistry | volume = 74 | issue = 9 | pages = 1848–1854 | year = 2010 | pmid = 20834152 | doi = 10.1271/bbb.100249 | doi-access = free }} In addition, an in silico examination from the Global Ocean Metagenomic Survey found 20 new lantibiotic cyclases.{{cite journal | vauthors = Li B, Sher D, Kelly L, Shi Y, Huang K, Knerr PJ, Joewono I, Rusch D, Chisholm SW, van der Donk WA | display-authors = 6 | title = Catalytic promiscuity in the biosynthesis of cyclic peptide secondary metabolites in planktonic marine cyanobacteria | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 107 | issue = 23 | pages = 10430–10435 | date = June 2010 | pmid = 20479271 | pmc = 2890784 | doi = 10.1073/pnas.0913677107 | doi-access = free | bibcode = 2010PNAS..10710430L }}

Posttranslational modification of proteins with phosphate groups by kinases is a key regulatory step throughout all biological systems. Phosphorylation events, either phosphorylation by protein kinases or dephosphorylation by phosphatases, result in protein activation or deactivation. These events have an impact on the regulation of physiological pathways, which makes the ability to dissect and study these pathways integral to understanding the details of cellular processes. There exist a number of challenges—namely the sheer size of the phosphoproteome, the fleeting nature of phosphorylation events and related physical limitations of classical biological and biochemical techniques—that have limited the advancement of knowledge in this area.{{cite journal | vauthors = Tarrant MK, Cole PA | title = The chemical biology of protein phosphorylation | journal = Annual Review of Biochemistry | volume = 78 | pages = 797–825 | year = 2009 | pmid = 19489734 | pmc = 3074175 | doi = 10.1146/annurev.biochem.78.070907.103047 }}

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 {{cite journal | vauthors = Wilson KP, McCaffrey PG, Hsiao K, Pazhanisamy S, Galullo V, Bemis GW, Fitzgibbon MJ, Caron PR, Murcko MA, Su MS | display-authors = 6 | title = The structural basis for the specificity of pyridinylimidazole inhibitors of p38 MAP kinase | journal = Chemistry & Biology | volume = 4 | issue = 6 | pages = 423–431 | date = June 1997 | pmid = 9224565 | doi = 10.1016/S1074-5521(97)90194-0 | doi-access = free }} 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,{{cite journal | vauthors = Pargellis C, Tong L, Churchill L, Cirillo PF, Gilmore T, Graham AG, Grob PM, Hickey ER, Moss N, Pav S, Regan J | display-authors = 6 | title = Inhibition of p38 MAP kinase by utilizing a novel allosteric binding site | journal = Nature Structural Biology | volume = 9 | issue = 4 | pages = 268–272 | date = April 2002 | pmid = 11896401 | doi = 10.1038/nsb770 | s2cid = 22680843 }}{{cite journal | vauthors = Schindler T, Bornmann W, Pellicena P, Miller WT, Clarkson B, Kuriyan J | title = Structural mechanism for STI-571 inhibition of abelson tyrosine kinase | journal = Science | volume = 289 | issue = 5486 | pages = 1938–1942 | date = September 2000 | pmid = 10988075 | doi = 10.1126/science.289.5486.1938 | s2cid = 957274 | bibcode = 2000Sci...289.1938S }} 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.{{cite journal | vauthors = Parang K, Till JH, Ablooglu AJ, Kohanski RA, Hubbard SR, Cole PA | title = Mechanism-based design of a protein kinase inhibitor | journal = Nature Structural Biology | volume = 8 | issue = 1 | pages = 37–41 | date = January 2001 | pmid = 11135668 | doi = 10.1038/83028 | s2cid = 12994600 }} Research groups also utilized ATP analogs as chemical probes to study kinases and identify their substrates.{{cite journal | vauthors = Fouda AE, Pflum MK | title = A Cell-Permeable ATP Analogue for Kinase-Catalyzed Biotinylation | journal = Angewandte Chemie | volume = 54 | issue = 33 | pages = 9618–9621 | date = August 2015 | pmid = 26119262 | pmc = 4551444 | doi = 10.1002/anie.201503041 }}{{cite journal | vauthors = Senevirathne C, Embogama DM, Anthony TA, Fouda AE, Pflum MK | title = The generality of kinase-catalyzed biotinylation | journal = Bioorganic & Medicinal Chemistry | volume = 24 | issue = 1 | pages = 12–19 | date = January 2016 | pmid = 26672511 | pmc = 4921744 | doi = 10.1016/j.bmc.2015.11.029 }}{{cite book | vauthors = Anthony TM, Dedigama-Arachchige PM, Embogama DM, Faner TR, Fouda AE, Pflum MK |chapter=ATP Analogs in Protein Kinase Research |pages=137–68 |doi=10.1002/9783527683031.ch6 | veditors = Kraatz HB, Sanela M |year=2015 |title=Kinomics: Approaches and Applications |publisher=Wiley |isbn=978-3-527-68303-1 }}

The development of novel chemical means of incorporating phosphomimetic 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.{{cite journal | vauthors = Muir TW, Sondhi D, Cole PA | title = Expressed protein ligation: a general method for protein engineering | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 95 | issue = 12 | pages = 6705–6710 | date = June 1998 | pmid = 9618476 | pmc = 22605 | doi = 10.1073/pnas.95.12.6705 | bibcode = 1998PNAS...95.6705M | doi-access = free }} In addition, researchers have used unnatural amino acid mutagenesis at targeted sites within a peptide sequence.{{cite journal | vauthors = Noren CJ, Anthony-Cahill SJ, Griffith MC, Schultz PG | title = A general method for site-specific incorporation of unnatural amino acids into proteins | journal = Science | volume = 244 | issue = 4901 | pages = 182–188 | date = April 1989 | pmid = 2649980 | doi = 10.1126/science.2649980 | bibcode = 1989Sci...244..182N }}{{cite journal | vauthors = Wang L, Xie J, Schultz PG | title = Expanding the genetic code | journal = Annual Review of Biophysics and Biomolecular Structure | volume = 35 | pages = 225–249 | year = 2006 | pmid = 16689635 | doi = 10.1146/annurev.biophys.35.101105.121507 }}

Advances in chemical biology have also improved upon classical techniques of imaging kinase action. For example, the development of peptide biosensors—peptides containing incorporated fluorophores improved temporal resolution of in vitro binding assays.{{cite journal | vauthors = Sharma V, Wang Q, Lawrence DS | title = Peptide-based fluorescent sensors of protein kinase activity: design and applications | journal = Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics | volume = 1784 | issue = 1 | pages = 94–99 | date = January 2008 | pmid = 17881302 | pmc = 2684651 | doi = 10.1016/j.bbapap.2007.07.016 }} 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.{{cite journal | vauthors = Violin JD, Zhang J, Tsien RY, Newton AC | title = A genetically encoded fluorescent reporter reveals oscillatory phosphorylation by protein kinase C | journal = The Journal of Cell Biology | volume = 161 | issue = 5 | pages = 899–909 | date = June 2003 | pmid = 12782683 | pmc = 2172956 | doi = 10.1083/jcb.200302125 }} FRET has also been used in tandem with Fluorescence Lifetime Imaging Microscopy (FLIM){{cite journal | vauthors = Verveer PJ, Wouters FS, Reynolds AR, Bastiaens PI | title = Quantitative imaging of lateral ErbB1 receptor signal propagation in the plasma membrane | journal = Science | volume = 290 | issue = 5496 | pages = 1567–1570 | date = November 2000 | pmid = 11090353 | doi = 10.1126/science.290.5496.1567 | bibcode = 2000Sci...290.1567V }} or fluorescently conjugated antibodies and flow cytometry{{cite journal | vauthors = Müller S, Demotz S, Bulliard C, Valitutti S | title = Kinetics and extent of protein tyrosine kinase activation in individual T cells upon antigenic stimulation | journal = Immunology | volume = 97 | issue = 2 | pages = 287–293 | date = June 1999 | pmid = 10447744 | pmc = 2326824 | doi = 10.1046/j.1365-2567.1999.00767.x }} to provide quantitative results with excellent temporal and spatial resolution.

Chemical biologists often study the functions of biological macromolecules using fluorescence techniques. The advantage of fluorescence versus other techniques resides in its high sensitivity, non-invasiveness, safe detection, and ability to modulate the fluorescence signal. In recent years, the discovery of green fluorescent protein (GFP) by Roger Y. Tsien and others, hybrid systems and quantum dots have enabled assessing protein location and function more precisely.{{cite journal | vauthors = Giepmans BN, Adams SR, Ellisman MH, Tsien RY | title = The fluorescent toolbox for assessing protein location and function | journal = Science | volume = 312 | issue = 5771 | pages = 217–224 | date = April 2006 | pmid = 16614209 | doi = 10.1126/science.1124618 | s2cid = 1288600 | bibcode = 2006Sci...312..217G }} Three main types of fluorophores are used: small organic dyes, green fluorescent proteins, and quantum dots. Small organic dyes usually are less than 1 kDa, and have been modified to increase photostability and brightness, and reduce self-quenching. Quantum dots have very sharp wavelengths, high molar absorptivity and quantum yield. Both organic dyes and quantum dyes do not have the ability to recognize the protein of interest without the aid of antibodies, hence they must use immunolabeling. Fluorescent proteins are genetically encoded and can be fused to your protein of interest. Another genetic tagging technique is the tetracysteine biarsenical system, which requires modification of the targeted sequence that includes four cysteines, which binds membrane-permeable biarsenical molecules, the green and the red dyes "FlAsH" and "ReAsH", with picomolar affinity. Both fluorescent proteins and biarsenical tetracysteine can be expressed in live cells, but present major limitations in ectopic expression and might cause a loss of function.

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.{{cite journal | vauthors = Michalet X, Pinaud FF, Bentolila LA, Tsay JM, Doose S, Li JJ, Sundaresan G, Wu AM, Gambhir SS, Weiss S | display-authors = 6 | title = Quantum dots for live cells, in vivo imaging, and diagnostics | journal = Science | volume = 307 | issue = 5709 | pages = 538–544 | date = January 2005 | pmid = 15681376 | pmc = 1201471 | doi = 10.1126/science.1104274 | bibcode = 2005Sci...307..538M }} 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.{{cite journal | vauthors = Terai T, Nagano T | title = Fluorescent probes for bioimaging applications | journal = Current Opinion in Chemical Biology | volume = 12 | issue = 5 | pages = 515–521 | date = October 2008 | pmid = 18771748 | doi = 10.1016/j.cbpa.2008.08.007 }}

Despite an increase in biological research within chemistry departments, attempts at integrating chemical biology into undergraduate curricula are lacking.{{cite journal | vauthors = Begley TP | title = Chemical biology: an educational challenge for chemistry departments | journal = Nature Chemical Biology | volume = 1 | issue = 5 | pages = 236–238 | date = October 2005 | pmid = 16408045 | doi = 10.1038/nchembio1005-236 | s2cid = 30591672 }} 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.{{Cite web |title=Coursework |url=https://www.acs.org/education/policies/acs-approval-program/guidelines/coursework.html |access-date=2023-12-02 |website=American Chemical Society |language=en}}

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.{{Cite web |title=Chemistry 461: Synthetic Chemical Biology {{!}} UBC Chemistry |url=https://www.chem.ubc.ca/chemistry-461-synthetic-chemical-biology-2324 |access-date=2023-12-02 |website=www.chem.ubc.ca}}

• Chemoproteomics
• Chemical genetics
• Chemogenomics

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• {{cite journal | vauthors = ((Dertinger SKW)), Chiu DT, Jeon NL, Whitesides GM | year = 2001 | title = Generation of gradients having complex shapes using microfluidic networks | journal = Analytical Chemistry | volume = 73 | issue = 6| pages = 1240–1246 | doi=10.1021/ac001132d}}
• {{cite journal | vauthors = Greif D, Pobigaylo N, Frage B, Becker A, Regtmeier J, Anselmetti D | title = Space- and time-resolved protein dynamics in single bacterial cells observed on a chip | journal = Journal of Biotechnology | volume = 149 | issue = 4 | pages = 280–288 | date = September 2010 | pmid = 20599571 | doi = 10.1016/j.jbiotec.2010.06.003 }}
• {{cite journal | vauthors = Li L, Ismagilov RF | title = Protein crystallization using microfluidic technologies based on valves, droplets, and SlipChip | journal = Annual Review of Biophysics | volume = 39 | pages = 139–158 | year = 2010 | pmid = 20192773 | doi = 10.1146/annurev.biophys.050708.133630 }}
• {{cite journal | vauthors = Lucchetta EM, Lee JH, Fu LA, Patel NH, Ismagilov RF | title = Dynamics of Drosophila embryonic patterning network perturbed in space and time using microfluidics | journal = Nature | volume = 434 | issue = 7037 | pages = 1134–1138 | date = April 2005 | pmid = 15858575 | pmc = 2656922 | doi = 10.1038/nature03509 | bibcode = 2005Natur.434.1134L }}
• {{cite journal | vauthors = Melin J, Quake SR | title = Microfluidic large-scale integration: the evolution of design rules for biological automation | journal = Annual Review of Biophysics and Biomolecular Structure | volume = 36 | pages = 213–231 | year = 2007 | pmid = 17269901 | doi = 10.1146/annurev.biophys.36.040306.132646 }}
• {{cite journal | vauthors = Shen F, Du W, Kreutz JE, Fok A, Ismagilov RF | title = Digital PCR on a SlipChip | journal = Lab on a Chip | volume = 10 | issue = 20 | pages = 2666–2672 | date = October 2010 | pmid = 20596567 | pmc = 2948063 | doi = 10.1039/c004521g }}
• {{cite journal | vauthors = Song H, Chen DL, Ismagilov RF | title = Reactions in droplets in microfluidic channels | journal = Angewandte Chemie | volume = 45 | issue = 44 | pages = 7336–7356 | date = November 2006 | pmid = 17086584 | pmc = 1766322 | doi = 10.1002/anie.200601554 }}
• {{cite journal | vauthors = Spiller DG, Wood CD, Rand DA, White MR | title = Measurement of single-cell dynamics | journal = Nature | volume = 465 | issue = 7299 | pages = 736–745 | date = June 2010 | pmid = 20535203 | doi = 10.1038/nature09232 | s2cid = 4426105 | bibcode = 2010Natur.465..736S }}
• {{cite journal | vauthors = Tice JD, Song H, Lyon AD, Ismagilov RF | title = Formation of droplets and mixing in multiphase microfluidics at low values of the Reynolds and the capillary numbers | journal = Langmuir | volume = 19 | issue = 22 | pages = 9127–9133 | year = 2003 | doi = 10.1021/la030090w }}
• {{cite journal | vauthors = Vincent ME, Liu W, Haney EB, Ismagilov RF | title = Microfluidic stochastic confinement enhances analysis of rare cells by isolating cells and creating high density environments for control of diffusible signals | journal = Chemical Society Reviews | volume = 39 | issue = 3 | pages = 974–984 | date = March 2010 | pmid = 20179819 | pmc = 2829723 | doi = 10.1039/b917851a }}
• {{cite journal | vauthors = Weibel DB, Whitesides GM | title = Applications of microfluidics in chemical biology | journal = Current Opinion in Chemical Biology | volume = 10 | issue = 6 | pages = 584–591 | date = December 2006 | pmid = 17056296 | doi = 10.1016/j.cbpa.2006.10.016 }}
• {{cite journal | vauthors = Whitesides GM | title = The origins and the future of microfluidics | journal = Nature | volume = 442 | issue = 7101 | pages = 368–373 | date = July 2006 | pmid = 16871203 | doi = 10.1038/nature05058 | s2cid = 205210989 | bibcode = 2006Natur.442..368W }}
• {{cite journal | vauthors = Young EW, Beebe DJ | title = Fundamentals of microfluidic cell culture in controlled microenvironments | journal = Chemical Society Reviews | volume = 39 | issue = 3 | pages = 1036–1048 | date = March 2010 | pmid = 20179823 | pmc = 2967183 | doi = 10.1039/b909900j }}

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• Cell Chemical Biology – An interdisciplinary journal that publishes papers of exceptional interest in all areas at the interface between chemistry and biology. [http://www.chembiol.com/ chembiol.com]
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• Wiley Encyclopedia of Chemical Biology [http://www.wiley.com/WileyCDA/WileyTitle/productCd-0471754773,descCd-description.html link]

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