New organic compounds are made by process of synthesis, in which more complex molecules are made from simpler starting molecules. Combinatorial chemistry is used to combine smaller molecules to produce one complex molecule.
When planning a synthesis, the target molecule must be identified. By looking at the functional groups it contains, chemists then work backwards using a sequence of logical reactions to produce suitable starting materials. This process is known as retrosynthesis.
The exact reagents required are identified when chemists disconnect the target molecules on paper to produce synthons, which are idealised fragments or ions. Each synthon has a synthetic equivalent which are the actual, existing compounds used to produce the target molecule.
There are several routes in an organic synthesis, and the most preferred is usually the fastest route. However in industrial processes this may not always be the case as other factors must be taken into consideration for example disposal of waste and health and safety concerns.
Getting The Right Isomer
When producing new compounds, some reactions produce a mixture of different isomers. This reduces the yield of the reaction and also means that there is the issue of having to separate the isomers.
These are three different isomers which can be produced from the nitration of methylbenzene. Separating them is difficult and time consuming. If enzymes are used to catalyse the reaction, they will be stereospecific, favouring the production of only one isomer.
Enzymes are biological catalysts which have specific three-dimentional shapes determined by the protein's structure. Competitive inhibitors have very similar three-dimensional shapes to the substrate and therefore have the specificity to bind to the active site of the enzyme. They don't react, however the block the active site so that it's no longer available to the substrate.
Molecular recognition is the interaction between the active site of an enzyme and the substrate. Very specific bonds are made between the two molecules leading to the production of a very specific product. The pharmacophore or certain compounds is known as the region which reacts with other compounds in order to initiate a reaction and produce the desired products. Many new drugs are designed on the basis of identifiying and isolating a certain pharmacophore.
Computer graphics can be used to produce a 3D map of the receptor site, meaning drugs with complementary pharmacophores can be synthesised. Computer modelling can also be used to ethically test and design medicines, as an alternative to animal testing or even human trials.