Chemical biology - Wikipedia
High-throughput screening assays for the identification of chemical probes. Nat Chem Biol Chemical genetics: Where genetics and pharmacology meet. The current meeting of chemistry conferences will be a multinational gathering and present major areas such as Medicinal Chemistry, Pharmaceutical Sciences. “chemical biology”, and “chemical genetics” are now fully incorporated into. A new chemical genetic approach based on covalent complementarity between Pharmacological approaches to studying protein kinases can be challenging to . region of c-Src (Met and Glu), while the sulfonamide group makes a.
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. 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.
Peptide synthesis In contrast to the traditional biotechnological practice of obtaining peptides or proteins by isolation from cellular hosts through cellular protein productionadvances in chemical techniques for the synthesis and ligation of peptides has allowed for the total synthesis of some peptides and proteins. 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 capabilities 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.
Given the widely recognized importance of proteins as cellular catalysts and recognition elements, the ability to precisely control the composition and connectivity of polypeptides is a valued tool in the chemical biology community and is an area of active research. While chemists have been making peptides for over years,  the ability to efficiently and quickly synthesize short peptides came of age with the development of Bruce Merrifield 's solid phase peptide synthesis SPPS.
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Prior to the development of SPPS, the concept of step-by-step polymer synthesis on an insoluble support was without chemical precedent. The development and "optimization" of SPPS took peptide synthesis from the hands of the specialized peptide synthesis community and put it into the hands of the broader chemistry, biochemistry, and now chemical biology community. SPPS is still the method of choice for linear synthesis of polypeptides up to 50 residues in length  and has been implemented in commercially available automated peptide synthesizers.
One inherent shortcoming in any procedure that calls for repeated coupling reactions is the buildup of side products resulting from incomplete couplings and side reactions.
This places the upper bound for the synthesis of linear polypeptide lengths at around 50 amino acids, while the "average" protein consists of amino acids. Although the shortcomings of linear SPPS were recognized not long after its inception, it took until the early s for effective methodology to be developed to ligate small peptide fragments made by SPPS, into protein sized polypeptide chains for recent review of peptide ligation strategies, see review by Dawson et al.
The oldest and best developed of these methods is termed native chemical ligation. Native chemical ligation was unveiled in a paper from the laboratory of Stephen B. Further refinements in native chemical ligation have allowed for kinetically controlled coupling of multiple peptide fragments, allowing access to moderately sized peptides such as an HIV-protease dimer  and human lysozyme.
Some of these drawbacks include the installation and preservation of a reactive C-terminal thioester, the requirement of an N-terminal cysteine residue which is the second-least-common amino acid in proteins and the requirement for a sterically unincumbering C-terminal residue.
This technique allows for access to much larger proteins, as only the N-terminal portion of the resulting protein has to be chemically synthesized. These techniques help to overcome the requirement of an N-terminal cysteine needed for standard native chemical ligation, although the steric requirements for the C-terminal residue are still limiting. A final category of peptide ligation strategies include those methods not based on native chemical ligation type chemistry.
Methods that fall in this category include the traceless Staudinger ligation,  azide-alkyne dipolar cycloadditions,  and imine ligations. Dawson, and Tom W. Muir, as well as many others involved in methodology development and applications of these strategies to biological problems. Protein design by directed evolution[ edit ] Main article: Directed evolution 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.
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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. Since only proteins with the desired activity are selected, multiple rounds of directed evolution lead to proteins with an accumulation beneficial traits.
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There are two general strategies for choosing the starting sequence for a directed evolution experiment: In a protein design experiment, an initial sequence is chosen at random and subjected to multiple rounds of directed evolution. For example, this has been employed successfully to create a family of ATP -binding proteins with a new folding pattern not found in nature. Among other things, this strategy has been used to successfully design four-helix bundle proteins.
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.
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. Computation has been used to design proteins with unnatural folds, such as a right-handed coiled coil. 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.
Szostak are significant researchers in this field. Biocompatible click cycloaddition reactions in chemical biology[ edit ] Recent advances in technology have allowed scientists to view substructures of cells at levels of unprecedented detail. Unfortunately these "aerial" pictures offer little information about the mechanics of the biological system in question. To be fully effective, precise imaging systems require a complementary technique that better elucidates the machinery of a cell.
By attaching tracking devices optical probes to biomolecules in vivo, one can learn far more about cell metabolismmolecular transportcell-cell interactions and many other processes  Bioorthogonal reactions[ edit ] 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. 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.
Design of bioorthogonal reagents and bioorthogonal chemical reporters[ edit ] The coupling of an optical 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, by definition, rapid, spontaneous, selective, and high-yielding.
Carolyn Bertozzi introduced inherent strain into the alkyne species by using a cyclic alkyne. In particular, cyclooctyne reacts with azido-molecules with distinctive vigor. When the probe is added to a biological system, it will selectively conjugate with the target molecule.
The most common method of installing bioorthogonal reactivity into a target biomolecule is through metabolic labeling. Cells are immersed in a medium where access to nutrients is limited to synthetically modified analogues of standard fuels such as sugars. As a consequence, these altered biomolecules are incorporated into the cells in the same manner as their wild-type brethren.
The optical probe is then incorporated into the system to image the fate of the altered biomolecules. Other methods of functionalization include enzymatically inserting azides into proteins and synthesizing phospholipids conjugated to cyclooctynes. More complex interactions have a smaller margin for error, so increased reaction efficiency is paramount to continued success in optically probing cellular machinery.
Also, by minimizing side reactions, the experimental design of a minimally perturbed living system is closer to being realized. Discovery of biomolecules through metagenomics[ edit ] Main article: Metagenomics The advances in modern sequencing technologies in the late s allowed scientists to investigate DNA of communities of organisms in their natural environments, so-called "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. These sources of eDNA include, but are not limited to, soilsocean, subsurfacehot springshydrothermal ventspolar ice capshypersaline habitats, and extreme pH environments. Goodman who are pioneers of metagenomics, explored metagenomic approaches toward the discovery of biologically active molecules such as antibiotics.
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.
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. For example, the Schipper group identified three eDNA derived AHL lactonases that inhibit biofilm formation of Pseudomonas aeruginosa via functional metagenomic assays.
As soon as the genes are sequenced, scientists can compare thousands of bacterial genomes simultaneously. These also led to the discovery of several novel proteins and small molecules.
For example, Banik et al. However, collaborative efforts from individuals from diverse fields including bacterial geneticsmolecular biologygenomicsbioinformaticsrobotssynthetic biologyand chemistry can solve this problem together and potentially lead to the discovery of many important biologically active molecules.
Phosphorylation events, either phosphorylation by protein kinases or dephosphorylation by phosphatasesresult in protein activation or deactivation.The Chemical Mind - Crash Course Psychology #3
These events have an immense 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.
A recent review  provides a detailed examination of the impact of newly developed chemical approaches to dissecting and studying biological systems both in vitro and in vivo. Through the use of a number of classes of small molecule modulators of protein kinases, chemical biologists have been able to gain a better understanding of the effects of protein phosphorylation.
For example, nonselective and selective kinase inhibitors, such as a class of pyridinylimidazole compounds described by Wilson, et al. 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 detailed knowledge of the chemical mechanism of kinase action with previously utilized inhibition motifs.
For example, Parang, et al. Many research groups utilized ATP analogs as a chemical probe to study kinases and identify their substrates. Historically, phosphorylation events have been studied by mutating an identified phosphorylation site serinethreonine or tyrosine to an amino acid, such as alaninethat cannot be phosphorylated.
While this approach has been successful in some cases, mutations are permanent in vivo and can have potentially detrimental effects on protein folding and stability. Thus, chemical biologists have developed new 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.
Protein semisynthesis, or more specifically expressed protein ligation EPLhas proven to be successful techniques for synthetically producing proteins that contain phosphomimetic molecules at either the C- or the N-terminus. For example, the development of peptide biosensors —peptides containing incorporated fluorophore molecules—allowed for improved temporal resolution in in vitro binding assays.
To utilize FRET for phosphorylation studies, fluorescent proteins are coupled to both a phosphoamino acid binding domain and a peptide that can by phosphorylated. Upon phosphorylation or dephosphorylation of a substrate peptide, a conformational change occurs that results in a change in fluorescence. Through the augmentation of classical biochemical methods as well as the development of new tools and techniques, chemical biologists have improved accuracy and precision in the study of protein phosphorylation.
Chemical approaches to stem-cell biology[ edit ] Main articles: Stem Cell and Induced stem cells Advances in stem-cell biology have typically been driven by discoveries in molecular biology and genetics.
These have included optimization of culture conditions for the maintenance and differentiation of pluripotent and multipotent stem-cells and the deciphering of signaling circuits that control stem-cell fate. However, chemical approaches to stem-cell biology have recently received increased attention due to the identification of several small molecules capable of modulating stem-cell fate in vitro.
Small molecules that modulate stem-cell behavior are commonly identified in high-throughput screens. Libraries of compounds are screened for the induction of a desired phenotypic change in cultured stem-cells. This is usually observed through activation or repression of a fluorescent reporter or by detection of specific cell surface markers by FACS or immunohistochemistry.
Hits are then structurally optimized for activity by the synthesis and screening of secondary libraries. The cellular targets of the small molecule can then be identified by affinity chromatographymass spectrometryor DNA microarray.
In the early days of toxicological pathology, pathologists often worked independently. Their evaluations of chemical-induced changes were limited to morphologic observations made at necropsy and during microscopic examination of tissue sections.
Toxicological pathology continues to evolve and the skills of the toxicological pathologist are keeping pace with this evolution. The result is high-quality and timely data that contributes to more informed decisions for clinical programs and regulations and ultimately leads to improvement of human, animal, and environmental health. Forensic Toxicology Forensic toxicologist deal with substances in the body that may have contributed to the crime, such as: Forensic toxicologists also work on cases involving environmental contamination, to determine the impact of chemical spills on nearby populations.
The analysis of illicit drugs is a challenge faced by forensics and toxicology laboratories. Confident drug metabolite identification of small molecules is the key to successful crime scene investigations.
Reproductive Toxicology Reproductive toxicology is a risk associated with some chemical substances that they will interfere in some way with usual reproduction. It includes adverse effects on sexual function and fertility in adult males and females. Several different effects which are unrelated to each other except in their outcome of lowered effective fertility. Reproductive toxicity from germ cell mutagenicity and carcinogenicity, even though both these hazards may also affect fertility.
Genetic info, programmed chemically in DNA, is conserved, simulated and transmitted to consecutive generations with high reliability. Toxicology Current Advances Toxicology Advances features the latest advances in various aspects of the experimental and biochemical effects which effects in the field of toxicology. The new technologies that are being harnessed to analyse and understand these events will also be studied by primary workers in the field.