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Virtual Screening- a Promising Approach to Drug DiscoveryBY: vanika garg | Category: Bioinformatics | Submitted: 2012-04-25 01:22:53
Article Summary: "Drug discovery and development is a chain process starting with target and lead discovery, followed by lead optimization and then clinical studies. It is the fastest growing industry. So the need of finding possible drug candidate is increasing exponentially. Out of number of techniques available,VS is increasingly gaining accep.."
Virtual Screening is a computational or in silico analog of Biological screening. It starts with a target and finally leads to discovery of lead compounds. It improves the quality of hits in High-throughput screening and can be performed without prior need of establishing an assay. It has been successfully used for the discovery of a drug named, Imatinib(magical drug or silver bullet). It was developed by Nicholas Lydon, Oregon Health and Science University for treatment of certain cancers.
Virtual Screening is a process of automatic evaluation of very large libraries of chemical compounds and chemical structures to find the possible drug candidates. It comprises a large variety of computational tools to select potentially active and bioavailable compounds, ranging from fast similarity filters to precise docking techniques. With VS it is even possible to investigate compounds that have not been synthesized yet. Virtual screening is knowledge-driven i.e. some information is available regarding either the nature of receptor binding pocket or type of ligand that is known to bind to it or both.
•If the receptor site geometry is known, the problem is to find a molecule that satisfies geometric constraints and is a good chemical match and
•If it is unknown, then the design should be based on other ligand molecules that bind well to the site.
Types of VS:
Based on whether the three-dimensional structure of target protein is available or not, there are two distinct methods available for virtual screening.
1.Ligand Similarity based virtual screening
Experimental determination of protein structures is a difficult task and is not routinely possible. Therefore, the situation that the structure of the target is unknown is very common at an early stage of drug discovery. In such cases, the help is taken from structures of those molecules which are already known to bind to the target.
According to the Biophysicists, when a molecule binds to the protein , it adopts a conformation that sterically and electrostatically fits into the active site. In order to detect compounds which can bind into the same active site, molecules having conformations similar to a given molecule can be searched. This information can be generated with the help of a number of programs which are based on the type of similarity measures chosen. e.g. Topological pharmacophores, feature trees which describe the overall topology of a molecule and can be used to perform similarity calculations.
2.Structure based virtual screening: -
When the structure of the target is known, the compounds are selected based on their fit into the active site of a protein. It has two important elements. First is, Docking that is how the ligand interacts with the receptor and fits into it. Another is Scoring, which provides a measure of given ligand will interact with a particular receptor using different score functions.
Structure based VS begins with determination of structure of receptor, finding a set of ligands that bind to the receptor and choosing the conformation with minimum energy levels. A number of soft wares like AutoDock, GOLD, GLIDE, ICM are used for this purpose.
Virtual Screening has its major application in
Ranking compounds for subsequent analysis and thus selecting the most active structures for a biological assay.
Assessing the probability that a given structure will exhibit a given activity.
Analyzing the results of High throughput screening runs.
Analyzing diverse molecular properties of lead compounds including Chemical Reactivity and its ADMET (absorption, distribution, metabolism, excretion, toxicity) properties.
Despite of its advantages ,application of VS is still limited because of its computationally intensive nature .V.S. can never substitute the real screening , its performance can only be validated in parallel with High Throughput Screening.
About Author / Additional Info:
A post graduate bioinformatics student ....
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