With the continuously increasing need for new drugs, bioinformatics has opened the doors to computer aided drug design (CAD) which provides the development of novel therapeutic drugs. The drugs we see today in market are being improved with the use of CAD and new and better medicinal drugs are being developed keeping in mind the needs of the time.

CAD utilizes the basic knowledge of protein-receptor chemistry and bioinformatics to design drugs with the use of web-based tools and databases. The key factors involved in drug design include a receptor molecule and a protein molecule. To make it a bit simpler, try recalling the lock-and-key hypothesis for enzyme functioning. The lock-and-hypothesis states that a receptor is complementary to a particular protein and when these two bind, conformational changes occur within the protein. Due to these conformational changes within the protein molecule, the protein either gets deactivated or activated, depending on the state that it was in earlier. When the enzyme dissociates from the protein molecule at a later point of time, the protein retains its older configuration and confirmation. So by applying this knowledge to CAD, one can state that the same happens when a receptor binds with a protein. A protein has some specific receptors and only those receptors that are specific to it can bind to that protein.

Protein-receptor specificity is indeed an interesting topic. Each protein has some specific receptors with which it binds. In the context of CAD, we will be using the term ligand for receptors. When a protein-ligand interaction occurs, conformational changes take place within the protein molecule. For a binding to occur between protein and ligand, specific amount of energy is required that is termed as binding energy. During the binding, the particular amount of energy is released that is known as activation energy. For molecules that are less likely to bind together or have weak chemical interactions mixtures between them, more binding energy is required. Molecules having strong chemical interactions need quite a lower amount of energy. Binding affinity is another term that indicates the extent of binding; the more the binding affinity the better the molecules bind.

To design a drug, first of all, mostly a protein molecule is determined that has to be targeted. This source of this protein molecules varies depending on the nature of the research. Usually a disease is targeted for which the drug is to be designed; then the disease causing pathogen or virus is identified that is later submitted to a biological lab to get genome information. The genome could be fed to any of the bioinformatics tools that provide the required data e.g. chem genome 3.0. The binding sites are identified by automatic binding site (active sites) prediction. In the continuation, protein coding sites are identified and then the data is fed to ASF as input in the form of protein structure. There are cases when the receptor molecule is available or the ligand and the search is for a suitable binding molecule.

Databases are available that provide access to millions of protein and ligand molecules. Some of them are RCSB and zinc database. Molecules are screened against a large library of compounds to get the molecules that bind with high affinity to the protein/receptor. Usually high binding affinity molecules are preferred.

Docking basically means binding of a protein and receptor molecules. The protein molecule is screened against a million compound library of ligand molecules. The data obtained is further fed into docking softwares like DOCK or AUTODock, to perform the docking. The results are analysed on the basis of binding affinity and other parameters. The protein-ligand molecules with the highest binding affinities are selected and then analysed for further processing. The complex should have the highest binding affinity possible in order to make the perfect drug. A good drug should have high specificity to its target. If a drug is not highly specific to its target, the results could be disastrous and there maybe side effects too.

A basic understanding of the concepts of drug design doesn't take much time. And See! It can be simple to grasp too. Sure it provides not only an insight in the typical mechanisms underlying the drug designing, but also provides a general overview of the whole concept. As I'd say, "From a disease causing bacteria-through genome-target drug". Although the deep understanding of the concepts of drug designing can be a lot tougher and a beginner would think a hundred times before dwelling into them, a basic overview understanding of these concepts sure isn't gonna hurt. Ciao.

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A Budding biotechnologist + writer from India.. Visit http://in.linkedin.com/pub/shivani-sharma/4b/91b/384 or refer cv.napping@gmail.com for more details.
Researcher ID- J-4200-2012