Drug Design and Discovery

How are drugs created or discovered? Natural drug products have been used for millenia Synthetic drugs came into being during the 19 th century Today, drugs are still come from this two sources Chemicals found in nature or synthesized in labs are randomly screened for their therapeutic ability

Atropine from Nightshade (Belladonna)Quinine from Cinchona bark Morphine from PoppiesTaxol from Yew Trees Drugs from Natural Sources

Salvarsan Drugs from Artificial Sources Acetaminophen Ibuprophen

Problems are: Long design cycle of 7-12 years High cost approximately $350 million per marketed drug Salvarsan, the first chemtherapeutic, was the 606 th compound tested by Dr. Ehrlich in over three years of study of syphilis

One way to increase the odds of finding a drug is through High Throughput Screening (HTS) HTS seeks to increase the number of compounds tested at one time for drug-like properties By testing 100s to 1000s of compounds at one time, HTS allows a drug company to search through many compounds in less time Potential compounds are screened using plates capable of holding 96 to over 3000 different compounds

HTS relies on small samples rapidly tested usually by robot The test or assay used depends on the type of drug required The assay must be simple to perform and easily detected by a robot, the assay also must be able to be performed in a small volume 2 to 200 l These assays often involve the measurement of luminescence, fluorescence, or absorbance, all of which are easily quantifiable

What are the targets of the drugs developed or what do they screen against? Traditionally drugs were first tested against an animal or a human who had the disease the company is interested in creating a drug against This is expensive, time consuming & can be dangerous While this is still done, it is done at a much later stage in the drug development Some HTS assays use cells, but many are cell-free or in vitro There are some HTS assays though that use organisms, but these are mainly flies, worms, or fish

96, 384, & 1536 well plates Hold 100, 20, 2 l/well respectively Assay Plates

3456-well plate, each well holds 200nl

Robot pipetting samples into a 96 well plate

Robot moving plates for screening

Large scale robotic screening area

Zebrafish in the well of a 96-well plate

Current ultra-HTS (uHTS) systems are capable of screening 100,000 to 200,000 compounds per day GlaxoSmithKline just opened a new center capable of screening 300,000 compounds against multiple targets per day Where do companies get all these different compounds?

Combinatorial Libraries

Combinatorial libraries are large collections of randomly generated compounds usually based on a scaffold molecule The scaffold molecule often is the skeleton of a known class of drugs or a random chemical structure The scaffold molecule is modified by the addition of functional groups such as methyl, ethyl, amino, or carboxyl groups Libraries can contain anywhere from 500 to 50,000 randomly generated members These libraries are then screened for possible drug compounds

Examples of basic scaffolds of an indole library R- groups represent regions which would be varied to create up to 40,000 discrete molecules

Libraries are screened to find hits Hits are active samples that meet a defined success criteria These criteria are determined by the company and are specific to the assay being used Once these hits are validated, meaning the compounds nature is confirmed, they progress to lead compound status A lead compound is a hit with sufficient potential to progress to full drug development

The lead compound then progresses to the next phase of drug development Where other aspects of its physical nature are tested The compound is assayed for toxicity, often this is done during HTS, but further tests are required in cells or whole organisms This is also when it will be determined how the drug is to be delivered

It was originally thought that combination of chemistry, robotics, & computers would deliver blockbuster drugs However, HTS of random compounds has not delivered a large number of new blockbuster drugs Companies are now taking known drugs or compounds that have drug-like properties & using these as scaffolds to create libraries These libraries are more focused in that they are tailored to the disease being targeted Another option is rational or structure based drug design

Rational Drug Design Engineering of a molecule or protein through specific changes such that it becomes drug-like Often requires choosing a target molecule in the cell, such as a receptor or enzyme and designing a therapeutic that prevents the target from causing or contributing to a disease Need to know the structure of the target usually obtained through X-ray crystallography or NMR Also need a complete understanding of the thermodynamics factors involved in binding, which vary from interaction to interaction

The target (green) has a very distinct shape to which the drug can bind The molecule shown, has a shape which would allow it to fit into the binding site Once a drug designer knows this, he can use this molecule as a base to build his drug By attaching methyl groups, carboxyl groups, etc. he can change the action the drug will induce

Starting molecule loosely binds to receptor As the molecule is modified it binds tighter to the receptor Eventually the designed molecule binds so tightly that it prevents the natural compound from binding Starting compound Final compound

AIDS drug nelfinavir (Viracept) is one of the few drugs on the market that can be traced directly to structure-based methods Here, the molecule is shown in the active site of HIV-1 protease

Other methods of drug design are based on taking known drugs & modifying their structure to make them better This requires one to know the structure of the drug Alterations may: Cause the drug to be more potent Give the drug fewer side effects Increase its solubility, giving better absorption

Meperidine has only 2 rings instead of 4, but it maintains strong analgesic activity It has better oral absorption than morphine, and shows less GI side effects

Another method of drug design is to take a known molecule & design a drug mimic A mimic looks like the endogenous molecule, but is not processed by the cell the same way These mimics work either as antagonists, that prevent cell functions Or agonists that turn on cellular function in the absence of the normal signal

Sildenfil was designed to mimic cGMP & be an antihypertensive or an anti-angina cGMP leads to, among other things, vascular relaxation which allows more blood to flow through vessels

Phosphodiesterase (PDE), is the enzyme that converts cGMP to GMP By blocking PDE-5, sildenafil prevents the breakdown of cGMP Leading to more blood in the vessels Unfortunately sildenafil did not work as well as the normal treatment, nitroglycerine But its side effect was much more promising…

Rational Protein Modification Involves taking a known therapeutic protein and optimizing it to function as a drug Even though the endogenous protein functions well in the cell, there are properties unique to being a drug which can be added to improve its therapeutic nature

PEG=polyethylene glycol