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.
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 through cyclization reactions. The term is a portmanteau of the words lactone + amide.
PyBOP is a reagent used to prepare amides from carboxylic acids and amines in the context of peptide synthesis. It can be prepared from 1-hydroxybenzotriazole and a chlorophosphonium reagent under basic conditions. It is a substitute for the BOP reagent that avoids the formation of the carcinogenic waste product HMPA. Thermal hazard analysis by differential scanning calorimetry (DSC) shows PyBOP is potentially explosive.
Pseudoproline derivatives are artificially created dipeptides to minimize aggregation during Fmoc solid-phase synthesis of peptides.
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) is a reagent commonly used for the synthesis of amides from carboxylic acids and amines in peptide synthesis. It can be prepared from 1-hydroxybenzotriazole and a chlorophosphonium reagent under basic conditions. This reagent has advantages in peptide synthesis since it avoids side reactions like the dehydration of asparagine or glutamine redisues. BOP has used for the synthesis of esters from the carboxylic acids and alcohols. BOP has also been used in the reduction of carboxylic acids to primary alcohols with sodium borohydride (NaBH4). Its use raises safety concerns since the carcinogenic compound HMPA is produced as a stoichiometric by-product.
N,N′-Diisopropylcarbodiimide is a carbodiimide used in peptide synthesis. As a liquid, it is easier to handle than the commonly used N,N′-dicyclohexylcarbodiimide, a waxy solid. In addition, N,N′-diisopropylurea, its byproduct in many chemical reactions, is soluble in most organic solvents, a property that facilitates work-up.
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 (N,N-diisopropylethylamine), 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 racemization that can otherwise occur during the reaction.
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 amidinium 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 HCTU and related reagents containing the 6-chloro-1-hydroxybenzotriazole moiety can be prepared by reaction with TCFH under basic conditions. It can exist in an N-form (guanadinium) or an O-form (uronium), but the N-form is generally considered to be more stable for this class of reagent. In vivo dermal sensitization studies according to OECD 429 confirmed HCTU is a strong skin sensitizer, showing a response at 0.50 wt% in the Local Lymph Node Assay (LLNA) placing it in Globally Harmonized System of Classification and Labelling of Chemicals (GHS) Dermal Sensitization Category 1A.
In organic chemistry, an active ester is an ester functional group that is highly susceptible toward nucleophilic attack. Activation can be imparted by modifications of the acyl or the alkoxy components of a normal ester, say ethyl acetate. Typical modifications call for electronegative substituents. Active esters are employed in both synthetic and biological chemistry.
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.
TCFH is an electrophilic amidine reagent used to activate a number of functional groups for reaction with nucleophilies. TCFH is most commonly used to activate carboxylic acids for reaction with amines in the context of amide bond formation and peptide synthesis.
