Most commonly, drugs are organic small molecules produced through chemical synthesis, but biopolymer-based drugs (also known as biologics) produced through biological processes are becoming increasingly more common. Sequence homology is often used to identify such risks. In addition, these drugs should also be designed so as not to affect any other important “off-target” molecules or antitargets that may be similar in appearance to the target molecule, since drug interactions with off-target molecules may lead to undesirable side effects. Another approach may be to enhance the normal pathway by promoting specific molecules in the normal pathways that may have been affected in the diseased state. Drugs may be designed that bind to the active region and inhibit this key molecule. Some approaches attempt to inhibit the functioning of the pathway in the diseased state by causing a key molecule to stop functioning. Typically a drug target is a key molecule involved in a particular metabolic or signaling pathway that is specific to a disease condition or pathology or to the infectivity or survival of a microbial pathogen. These other characteristics are often difficult to optimize using rational drug design techniques.
Although modeling techniques for prediction of binding affinity are reasonably successful, there are many other properties, such as bioavailability, metabolic half-life, lack of side effects, etc., that first must be optimized before a ligand can become a safe and efficacious drug. What is really meant by drug design is ligand design (i.e., design of a small molecule that will bind tightly to its target). The phrase “drug design” is to some extent a misnomer. Finally, drug design that relies on the knowledge of the three-dimensional structure of the biomolecular target is known as structure-based drug design. This type of modeling is often referred to as computer-aided drug design.
Drug design frequently but not necessarily relies on computer modeling techniques. In the most basic sense, drug design involves the design of small molecules that are complementary in shape and charge to the biomolecular target with which they interact and therefore will bind to it. 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, 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.
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