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The reaction can be driven to completion and high yields through the use of excess reagent. In this method, building blocks are protected at all reactive functional groups. The order of functional group reactions can be controlled by the order of deprotection. This method is used for the synthesis of peptides,[1][2] deoxyribonucleic acid (DNA), ribonucleic acid (RNA), and other molecules that need to be synthesised in a certain alignment.[3] More recently, this method has also been used in combinatorial chemistry and other synthetic applications. The process was originally developed in the 1950s and 1960s by Robert Bruce Merrifield in order to synthesise peptide chains,[4] and which was the basis for his 1984 Nobel Prize in Chemistry.[5]
In the basic method of solid-phase synthesis, building blocks that have two functional groups are used. One of the functional groups of the building block is usually protected by a protective group. The starting material is a bead which binds to the building block. At first, this bead is added into the solution of the protected building block and stirred. After the reaction between the bead and the protected building block is completed, the solution is removed and the bead is washed. Then the protecting group is removed and the above steps are repeated. After all steps are finished, the synthesised compound is chemically cleaved from the bead.
If a compound containing more than two kinds of building blocks is synthesised, a step is added before the deprotection of the building block bound to the bead; a functional group which is on the bead and did not react with an added building block has to be protected by another protecting group which is not removed at the deprotective condition of the building block. Byproducts which lack the building block of this step only are prevented by this step. In addition, this step makes it easy to purify the synthesised compound after cleavage from the bead.
Solid-phase peptide synthesis (SPPS)
Solid-phase synthesis is a common technique for peptide synthesis. Usually, peptides are synthesised from the carbonyl group side (C-terminus) to amino group side (N-terminus) of the amino acid chain in the SPPS method, although peptides are biologically synthesised in the opposite direction in cells. In peptide synthesis, an amino-protected amino acid is bound to a solid phase material or resin (most commonly, low cross-linked polystyrene beads), forming a covalent bond between the carbonyl group and the resin, most often an amido or an ester bond.[6] Then the amino group is deprotected and reacted with the carbonyl group of the next N-protected amino acid. The solid phase now bears a dipeptide. This cycle is repeated to form the desired peptide chain. After all reactions are complete, the synthesised peptide is cleaved from the bead.
The protecting groups for the amino groups mostly used in the peptide synthesis are 9-fluorenylmethyloxycarbonyl group (Fmoc) and t-butyloxycarbonyl (Boc). A number of amino acids bear functional groups in the side chain which must be protected specifically from reacting with the incoming N-protected amino acids. In contrast to Boc and Fmoc groups, these have to be stable over the course of peptide synthesis although they are also removed during the final deprotection of peptides.
Relatively short fragments of DNA, RNA, and modified oligonucleotides are also synthesised by the solid-phase method. Although oligonucleotides can be synthesised in a flask, they are almost always synthesised on solid phase using a DNA/RNA synthesizer. For a more comprehensive review, see oligonucleotide synthesis. The method of choice is generally phosphoramidite chemistry, developed in the 1980s.
Solid-phase organic synthesis
Solid-phase synthesis techniques have historically been used primarily in biochemical settings with a strong focus on peptide couplings. However, developents in the late 1980s and early 1990s demonstrated the enhanced efficiency and selectivity of many reactions in the solid state. Perhaps most notably, Fumio Toda authored and co-authored numerous papers on the topic[1,2,3] and developed many attractive protocols for previously tedious reactions [4,5]. In fact, many air and moisture sensitive reactions and reagents can be used without the necessisty of typical air and moisture techniques[6-18] due to the greatly decreased diffusivity of vapors through nonporous solid mixtures as opposed to liquid mixtures. The lack of porosity in any given solid-phase organic reaction mixture is owed to the extremely low particle size obtained upon grinding with a mortar and pestle or ball mill, the former of which allows for much faster reaction times, while the latter facilitates the use of solid-state chemistry by untrained operators. In practice, the technique by which reactants are ground in a mortar and pestle is both simple and intuitive, and can be derived autonomously without instruction simply by finding the most ergonomically favorable grinding technique (which is individual to each operator) and observing the mixture's particle size to ensure that any macroscopic particles are ground until microscopic. Further grinding reduces particle sizes to clusters of a few hundred atoms each, and these clusters of particles react with clusters containing compatible molecules to form new product molecules, which themselves possess their own crystal structure and must displace the parent particles to conform to such a structure. This displacement then propels the parent particles towards other similarly low-volume/high-surface area particles, resulting in a cascading collisions that greatly enhance reaction times. Organic reactions in the solid phase often proceed 50-100 times more quickly than their counterparts, with some even progressing 1200 times more quickly[19]. Solid-phase organic synthesis, while still discouraged by some chemists, boasts many advantages over solution phase reactions, most notably in its speed, selectivity, air and moisture tolerance, simplicity, environmental friendliness, safety, and accessibility. The source of the aversion to solid phase chemistry comes most likely from Aristotle's famous quote "No Coopora nisi Fluida", meaning "No reaction occurs in the absence of solvent". This statement was a hypothesis on the basis that meat stew spoiled while salted meat did not, milk itself spoiled while powdered milk did not, and crushed grapes gave wine while dried grapes did not. This hypothesis, like many in the chemical community, was accepted as gospel until a pioneering chemist proved it wrong, and to this day is still accepted by the majority of chemists simply due to their lack of knowledge of this development. Even for decades following the discovery of solid phase peptide synthesis, it was not developed for organic synthesis until the late 1980s, and was developed out of a serendipitous discovery (i.e. not inspired by the success solid-phase peptide synthesis). Even now, it is frowned upon by numerous renowned synthetic chemists simply on the basis that they are unfamiliar with it.
Combinatorial chemistry comprises chemical synthetic methods that make it possible to prepare a large number of compounds in a single process. These compound libraries can be made as mixtures, sets of individual compounds or chemical structures generated by computer software. Combinatorial chemistry can be used for the synthesis of small molecules and for peptides.
Elias James Corey is an American organic chemist. In 1990, he won the Nobel Prize in Chemistry "for his development of the theory and methodology of organic synthesis", specifically retrosynthetic analysis.
A protecting group or protective group is introduced into a molecule by chemical modification of a functional group to obtain chemoselectivity in a subsequent chemical reaction. It plays an important role in multistep organic synthesis.
A dipeptide is an organic compound derived from two amino acids. The constituent amino acids can be the same or different. When different, two isomers of the dipeptide are possible, depending on the sequence. Several dipeptides are physiologically important, and some are both physiologically and commercially significant. A well known dipeptide is aspartame, an artificial sweetener.
Hermann Emil Louis Fischer was a German chemist and 1902 recipient of the Nobel Prize in Chemistry. He discovered the Fischer esterification. He also developed the Fischer projection, a symbolic way of drawing asymmetric carbon atoms. He also hypothesized lock and key mechanism of enzyme action. He never used his first given name, and was known throughout his life simply as Emil Fischer.
Native Chemical Ligation (NCL) is an important extension of the chemical ligation concept for constructing a larger polypeptide chain by the covalent condensation of two or more unprotected peptides segments. Native chemical ligation is the most effective method for synthesizing native or modified proteins of typical size.
In organic chemistry, peptide synthesis is the production of peptides, compounds where multiple amino acids are linked via amide bonds, also known as peptide bonds. Peptides are chemically synthesized by the condensation reaction of the carboxyl group of one amino acid to the amino group of another. Protecting group strategies are usually necessary to prevent undesirable side reactions with the various amino acid side chains. Chemical peptide synthesis most commonly starts at the carboxyl end of the peptide (C-terminus), and proceeds toward the amino-terminus (N-terminus). Protein biosynthesis in living organisms occurs in the opposite direction.
Dess–Martin periodinane (DMP) is a chemical reagent used in the Dess–Martin oxidation, oxidizing primary alcohols to aldehydes and secondary alcohols to ketones. This periodinane has several advantages over chromium- and DMSO-based oxidants that include milder conditions, shorter reaction times, higher yields, simplified workups, high chemoselectivity, tolerance of sensitive functional groups, and a long shelf life. However, use on an industrial scale is made difficult by its cost and its potentially explosive nature. It is named after the American chemists Daniel Benjamin Dess and James Cullen Martin who developed the reagent in 1983. It is based on IBX, but due to the acetate groups attached to the central iodine atom, DMP is much more reactive than IBX and is much more soluble in organic solvents.
Benzyl chloroformate, also known as benzyl chlorocarbonate or Z-chloride, is the benzyl ester of chloroformic acid. It can be also described as the chloride of the benzyloxycarbonyl group. In its pure form it is a water-sensitive oily colorless liquid, although impure samples usually appear yellow. It possesses a characteristic pungent odor and degrades in contact with water.
The Robinson–Gabriel synthesis is an organic reaction in which a 2-acylamino-ketone reacts intramolecularly followed by a dehydration to give an oxazole. A cyclodehydrating agent is needed to catalyze the reaction It is named after Sir Robert Robinson and Siegmund Gabriel who described the reaction in 1909 and 1910, respectively.
Di-tert-butyl dicarbonate is a reagent widely used in organic synthesis. Since this compound can be regarded formally as the acid anhydride derived from a tert-butoxycarbonyl (Boc) group, it is commonly referred to as Boc anhydride. This pyrocarbonate reacts with amines to give N-tert-butoxycarbonyl or so-called Boc derivatives. These carbamate derivatives do not behave as amines, which allows certain subsequent transformations to occur that would be incompatible with the amine functional group. The Boc group can later be removed from the amine using moderately strong acids. Thus, Boc serves as a protective group, for instance in solid phase peptide synthesis. Boc-protected amines are unreactive to most bases and nucleophiles, allowing for the use of the fluorenylmethyloxycarbonyl group (Fmoc) as an orthogonal protecting group.
The tert-butyloxycarbonyl protecting group or tert-butoxycarbonyl protecting group is a protecting group used in organic synthesis.
Nucleoside phosphoramidites are derivatives of natural or synthetic nucleosides. They are used to synthesize oligonucleotides, relatively short fragments of nucleic acid and their analogs. Nucleoside phosphoramidites were first introduced in 1981 by Beaucage and Caruthers. To avoid undesired side reactions, reactive hydroxy and exocyclic amino groups present in natural or synthetic nucleosides are appropriately protected. As long as a nucleoside analog contains at least one hydroxy group, the use of the appropriate protecting strategy allows one to convert that to the respective phosphoramidite and to incorporate the latter into synthetic nucleic acids. To be incorporated in the middle of an oligonucleotide chain using phosphoramidite strategy, the nucleoside analog must possess two hydroxy groups or, less often, a hydroxy group and another nucleophilic group (amino or mercapto). Examples include, but are not limited to, alternative nucleotides, LNA, morpholino, nucleosides modified at the 2'-position (OMe, protected NH2, F), nucleosides containing non-canonical bases (hypoxanthine and xanthine contained in natural nucleosides inosine and xanthosine, respectively, tricyclic bases such as G-clamp, etc.) or bases derivatized with a fluorescent group or a linker arm.
Oligonucleotide synthesis is the chemical synthesis of relatively short fragments of nucleic acids with defined chemical structure (sequence). The technique is extremely useful in current laboratory practice because it provides a rapid and inexpensive access to custom-made oligonucleotides of the desired sequence. Whereas enzymes synthesize DNA and RNA only in a 5' to 3' direction, chemical oligonucleotide synthesis does not have this limitation, although it is most often carried out in the opposite, 3' to 5' direction. Currently, the process is implemented as solid-phase synthesis using phosphoramidite method and phosphoramidite building blocks derived from protected 2'-deoxynucleosides, ribonucleosides, or chemically modified nucleosides, e.g. LNA or BNA.
Richard A. Houghten is a heterocyclic organic chemist and founder of the journal Peptide Research, which was later merged with the International Journal of Peptide and Protein Research, to become the Journal of Peptide Research. His work mainly concerns peptide activity and pharmacology. He is the founder and president of the Torrey Pines Institute for Molecular Studies (TPIMS), a biomedical research institute. Houghten pioneered the "tea-bag" approach of producing peptides for pharmacological work.
Morten Peter Meldal is a Danish chemist and Nobel laureate. He is a professor of chemistry at the University of Copenhagen in Copenhagen, Denmark. He is best known for developing the CuAAC-click reaction, concurrently with but independent of Valery V. Fokin and K. Barry Sharpless.
Glycopeptides are peptides that contain carbohydrate moieties (glycans) covalently attached to the side chains of the amino acid residues that constitute the peptide.
The fluorenylmethoxycarbonyl protecting group (Fmoc) is a base-labile protecting group used in organic synthesis.
The split and pool (split-mix) synthesis is a method in combinatorial chemistry that can be used to prepare combinatorial compound libraries. It is a stepwise, highly efficient process realized in repeated cycles. The procedure makes it possible to prepare millions or even trillions of compounds as mixtures that can be used in drug research.
Leonidas Zervas was a Greek organic chemist who made seminal contributions in peptide chemical synthesis. Together with his mentor Max Bergmann they laid the foundations for the field in 1932 with their major discovery, the Bergmann-Zervas carboxybenzoxy oligopeptide synthesis which remained unsurpassed in utility for the next two decades. The carboxybenzyl protecting group he discovered is often abbreviated Z in his honour.
↑ Merrifield, Bruce Arthur (1963). "Solid Phase Peptide Synthesis. I. The Synthesis of a Tetrapeptide". J. Am. Chem. Soc. 85 (14): 2149–2154. doi:10.1021/ja00897a025.
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