Before the advent of the biotechnology revolution, diseases were not studied at the cellular or molecular level, and most drugs were developed through a combination of luck and intuition regarding the basis of drug function. Drug development incorporated a lot of screening work by biologists and chemists, and a number of chemicals synthesised by microorganisms, plants and chemists were screened for possible use.

Through such efforts pharmaceutical companies have collected a large database of compounds with hope of their use for one or other target. Development of a drug from potential compounds includes many steps relating to efforts to reduce side effects and improve pharmacological activity.

The goal of pharmacology is to design a chemical compound that would interact with characterised (target) receptor on a cell in a specific and predictable manner. It is only recently that information about the structure of receptors and other small molecules has become available. Most drug discovery programmes now combine rational drug-design, medicinal chemistry with sophisticated screening. Computer-aided compound design and chemical database searches help the medicinal chemist and pharmacologist to match structure with function to device novel organic therapeutics. X-ray crystallography can be applied to drugs for study of structure, but it is difficult to apply it to the receptors.

Interference in the body mechanisms to disturb the normal functioning is caused at certain levels when disease or disorder occurs. These levels obviously become the targets for efforts in drug designing.

Classes of Proteins that target  the living cell

Recent developments in molecular biology have provided several important techniques, which can be used to study interactions of drugs with specific membrane receptors.

Molecular biology has helped in predicting the complete amino acid sequence of receptors from clones isolated by using DNA probes coding for small peptides (receptor fragments) that have been purified and sequenced. This has helped to determine primary structure of several receptors. Since most receptors belong to same gene families, it has been possible to determine primary structure even of those receptors for which no amino acid sequence was available. Receptor proteins thus share certain conserved amino acid sequences. It has been now possible to group receptors into families based on their structures. This further groups them into gene families. Diversity of receptors from today's data suggests existence of four such gene families. However the diversity of receptors may be larger than anticipated.

Molecular biology can play a role in determining the structure of receptors, and screening drugs for interactions with specific receptors. It is essential to isolate receptor of interest from other receptor subtypes and to reconstitute the receptor into the functional environment. Cloning cDNA in proper mammalian cells and their expression can do this. This gives large amount of receptor protein for various studies. Study of structure can be done then. Also sufficient amount of membranes can be obtained from such expressed mammalian cells to use them for filter binding assays with radioactive ligands. Same cells can be characterised electro-physiologically using sensitive patch-clamp technique and drugs can be rapidly applied over the whole cell surface.

Molecular biology plays role in characterising drug-binding sites. The availability of cloned DNA and the ability to express receptors at high levels provides an experimental framework in which the structure of receptor can be studied by making changes in the receptor through in vitro mutagenesis. Then the effect of changes can be studied at the level of binding and coupling studies. Molecular biology techniques will be applied in combination with traditional biochemical and biophysical techniques to provide large amounts of receptor proteins necessary for structural studies.

Biotechnology companies have used the power of genetic engineering to develop understanding of a disease state at molecular level. Mapping the molecular pathology of a disease by genetic analysis allows the identification of the molecules in a cellular cascade that results in diseased cell or tissue. Targets may include genes, gene regulatory factors, gene products (including enzymes, regulatory and signalling proteins), and both intracellular and extracellular receptors. The ability to clone, express and isolate virtually any desired targets has led to explosion in target strategies. Biotechnology companies are developing large number of molecules that moderate effects of target molecules. Biotechnology companies have developed rapid in vitro methods for generating, screening and amplifying drug candidate molecules using the same building blocks of life – nucleic acids, amino acids and small organic molecules. The goal of this technology is also to explore three-dimensional 'shape space' of the targets for requisite affinity and specificity. At molecular level this means determining steric and electronic complementarity between target and drug.

High-throughput screening systems exemplified by DNA chips are poised to significantly impact the drug discovery processes. DNA microarray systems coupled with high-throughput robotics will enable parallel analysis of a large population of genetic targets. DNA arrays will shift the paradigm of drug development by impacting the traditional bottlenecks of drug discovery. Pharmacogenetics will help identify novel targets for the drug development process by pairing gene expression to the onset and progression of disease, thereby providing increased small and macromolecule drug targets.

Pharmacogenomics on the other hand will identify individual genetic variations and their potential impact on drug activity. These technologies will expedite the drug development process and not only reduce the overall cost of development, but also bring safer, more effective drugs to the market sooner.

Let us see an example of application of DNA microarray system to understand how it helps in drug designing.

Drug Discovery by Microarray Gene Response Profiling

A microarray containing each of the open reading frames of the M. tuberculosis genome was prepared and used to identify genes that are selectively expressed or repressed by exposure of the organism to inhibitors of mycolic acid synthesis, including isoniazid (INH). Genes encoding components of the FASII pathway were selectively induced indicating that the gene response profile is pathway-specific. This general method can lead to the identification of the target of lead compounds whose mode-of-action is unknown and to the development of pathway-specific, high-throughput screens.

The work of mapping of genome of malarial parasite is completed. The understanding of the genes (their position in genome, their sequence etc.) of the malarial parasite which have active role in causing disease or responsible for development of drug resistance will help researchers to identify and validate good drug targets much more rapidly.