Computer Aided Drug Design: The Most Fundamental Goal is to Predict Whether a Given Molecule will Bind to a Target and if so How Strongly

Abstract

In the most basic sense, drug design involves the design of small molecules that are complementary in shape and charge to the bimolecular target with which they interact and therefore will bind to it. Drug design, sometimes referred to as rational drug design or more simply rational design is the inventive process of finding new medications based on the knowledge of a biological target. The drug is most commonly an organic small molecule that activates or inhibits the function of a biomolecule such as a protein, which in turn results in a therapeutic benefit to the patient. Drug design frequently but not necessarily relies on computer modeling techniques. This type of modeling is often referred to as computer-aided drug design. Finally, drug design that relies on the knowledge of the three-dimensional structure of the bimolecular target is known as structure-based drug design. Structure-based drug design (or direct drug design) relies on knowledge of the three dimensional structure of the biological target obtained through methods such as x-ray crystallography or NMR spectroscopy. If an experimental structure of a target is not available, it may be possible to create a homology of the target based on the experimental structure of a related protein. Using the structure of the biological target, candidate drugs that are predicted to bind with high affinity and selectivity to the target may be designed using interactive graphics and the intuition of a medicinal chemist. Alternatively various automated computational procedures may be used to suggest new drug candidates.

Keywords: Therapeutic, Three-dimensional structure, Rational drug design, Structure-based drug design, Crystallography and Spectroscopy.