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.
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.
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.
In chemistry, solid-phase synthesis is a method in which molecules are covalently bound on a solid support material and synthesised step-by-step in a single reaction vessel utilising selective protecting group chemistry. Benefits compared with normal synthesis in a liquid state include:
A lactam is a cyclic amide, formally derived from an amino alkanoic acid. The term is a portmanteau of the words lactone + amide.
In organic chemistry, a carbodiimide is a functional group with the formula RN=C=NR. They are exclusively synthetic. A well known carbodiimide is dicyclohexylcarbodiimide, which is used in peptide synthesis. Dialkylcarbodiimides are stable. Some diaryl derivatives tend to convert to dimers and polymers upon standing at room temperature, though this mostly occurs with low melting point carbodiimides that are liquids at room temperature. Solid diaryl carbodiimides are more stable, but can slowly undergo hydrolysis in the presence of water over time.
PyBOP is a peptide coupling reagent used in solid phase peptide synthesis. It is used as a substitute for the BOP reagent - avoiding the formation of the carcinogenic waste product HMPA.
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.
N-Hydroxysuccinimide (NHS) is an organic compound with the formula (CH2CO)2NOH. It is a white solid that is used as a reagent for preparing active esters in peptide synthesis. It can be synthesized by heating succinic anhydride with hydroxylamine or hydroxylamine hydrochloride.
BOP (benzotriazol-1-yloxytris(dimethylamino)phosphonium hexafluorophosphate) reagent is a reagent commonly used in the synthesis of peptides. Its use is discouraged because coupling using BOP liberates HMPA which is carcinogenic, although for small scale use in an organic laboratory this is not a great disadvantage as it is in large scale industrial usage. BOP has been used for peptide coupling, synthesis of esters, esterification of carboxylic acids, or as a catalyst. This reagent is advantageous in peptide coupling to other derived reagents because there are no side reactions from the dehydration of asparagine or glutamine. In peptide coupling the BOP reagent works well because it forms reactive intermediates which allow for the amines to bond together with little energy loss. In the reduction of carboxylic acids, using the BOP reagent with NaBH4 resulted in high percent yields.
HATU is a reagent used in peptide coupling chemistry to generate an active ester from a carboxylic acid. HATU is used along with Hünig's base, or triethylamine to form amide bonds. Typically DMF is used as solvent, although other polar aprotic solvents can also be used.
1-Hydroxy-7-azabenzotriazole (HOAt) is a triazole used as a peptide coupling reagent. It suppresses the racemization.
Triazolopyridines are a class of heterocyclic chemical compounds with a triazole ring fused to a pyridine ring. There are multiple isomers which differ by the location of the nitrogen atoms and the nature of the ring fusion.
In organic chemistry, phosphonium coupling is a cross-coupling reaction for organic synthesis. It is a mild, efficient, chemoselective and versatile methodology for the formation of C–C, C–N, C–O, and C–S bond of unactivated and unprotected tautomerizable heterocycles. The method was originally reported in 2004. The C–OH bond of a tautomerizable heterocycle is activated with a phosphonium salt, and subsequent functionalization with either a nucleophile through SNAr displacement or an organometallic through transition metal catalyzed cross coupling reaction. The in situ activation of the C-OH bond in phosphonium coupling has been applied to cross coupling reactions of tautomerizable heterocycles and arenols using other types of activating reagents.
DEPBT is a peptide coupling reagent used in peptide synthesis. It shows remarkable resistance to racemization.
HBTU is a coupling reagent used in solid phase peptide synthesis. It was introduced in 1978 and shows resistance against racemization. It is used because of its mild activating properties.
Ethyl cyanohydroxyiminoacetate (oxyma) is the oxime of ethyl cyanoacetate and finds use as an additive for carbodiimides, such as dicyclohexylcarbodiimide (DCC) in peptide synthesis. It acts as a neutralizing reagent for the basicity or nucleophilicity of the DCC due to its pronounced acidity and suppresses base catalyzed side reactions, in particular racemization.
HCTU is an aminium coupling reagent used in peptide synthesis. It is analogous to HBTU. The HOBt moiety has a chlorine in the 6 position which improves reaction rates and the synthesis of difficult couplings
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.
