Case 5.1 - DESIGNING DRUGS VIRTUALLY

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CASE STUDY 5.1
DESIGNING DRUG VIRTUALLY
CASE SUMMARY
Pharmaceutical companies and medical researcher are
constantly trying to find new drugs that will provide
better treatments especially for cancer and other
serious illness. Drug development, testing and
administration are information-intensive area with
varying computing needs.
In this case, the experience of the medical research
engaged in drug discovery by showing how
technology can benefit the business performance
through the acquisition and application of knowledge
in order to success and survive in all areas of business.
SUGGESTION AND ACTION
QUESTION
1. Why are computers so important in drug discovery?
2. What roles played by computers in the drug discovery process?

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1. Why are computers so important in drug discovery?
Previously, traditional methods of drug discovery rely on trial-and-error testing of chemical
substances on cultured cells or animals, and matching the apparent effects to treatments. The
traditional drug discovery processes are painstaking and complicated. It is take a lot of time
and a lot of process and too much trial-and-error.
Drug discovery and development is an intense, lengthy and an interdisciplinary endeavor.
Before the twentieth century, medicines consisted mainly of herbs and potions and it was not
until the mid-nineteenth century that the first serious efforts were made to isolate and purify
the active principles of these remedies. Drug development companies tried to speed up the
process by creating huge libraries of potential compounds and using robots to quickly review
hundreds of thousands of sample to see if any worked. For the pharmaceutical industry, the
number of years to bring a drug from discovery to market is approximately 12-14 years and
costing up to $ 1.2 - $ 1.4 billion dollars.
The use of complementary experimental and informatics techniques increases the chance of
success in many stages of the discovery process, from the identification of novel targets and
elucidation of their functions to the discovery and development of lead compounds with
desired properties. The researchers had no idea and not understand the “key” or the “lock”.
Scientists were used the powerful computers to analyze thousands of interference patterns.
Next, researchers must find a custom molecule to fit that particular “lock”. The molecule
must be able to bind to target, synthesized and manufactured in large quantities, and
metabolized by body at just the right rate.
Computation tools offer the advantage of delivering new drug candidates more quickly and at
a lower cost, discover of drug for rate and unusual disease treatment, accurate and efficient
process for developing effective medications and for understanding how drugs actually work.
Subsequently, researchers must find a custom molecule to fit that particular “lock”. This is
because the molecule must be able to bind to the target, synthesized and manufacture in large
quantity and metabolized by the body at just the right rate. That is why computers are so
important in the drug discovery process. Eventually, the high-powered computers help
evaluate the structures and properties of molecules that are most likely to bind to that target

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and rapidly search database libraries of chemical structures in order to identify the most
promising candidates.
Computer-aided drug design uses computational chemistry to discover, enhance, or study
drugs and related biologically active molecules. The most fundamental goal is to predict
whether a given molecule will bind to a target and if so how strongly. Molecular mechanics
or molecular dynamics are most often used to predict the conformation of the small molecule
and to model conformational changes in the biological target that may occur when the small
molecule binds to it. Semi-empirical, quantum chemistry methods, or density functional
theory are often used to provide optimized parameters for the molecular mechanics
calculations and also provide an estimate of the electronic properties (electrostatic potential,
Polari ability, etc.) of the drug candidate that will influence binding affinity.

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2. What roles played by computers in the drug discovery process?
Developing a new drug from original idea to the launch of a finished product is a complex
process which can take 12–15 years and cost in excess of $1 billion. The idea for a target can
come from a variety of sources including academic and clinical research and from the
commercial sector. It may take many years to build up a body of supporting evidence before
selecting a target for a costly drug discovery programmer. Once a target has been chosen, the
pharmaceutical industry and more recently some academic centers have streamlined a
number of early processes to identify molecules which possess suitable characteristics to
make acceptable drugs.
Generally, in the field of medicine, drug discovery is the process by which new candidate
medications are discovered. The objective of drug design is to find a chemical compound that
can fit to a specific cavity on a protein target both geometrically and chemically. It is
generally recognized that drug discovery and development are very time and resources
consuming processes.
There is an ever growing effort to apply computational power to the combined chemical and
biological space in order to streamline drug discovery, design, development and optimization.
In biomedical arena, computer-aided is being utilized to expedite and facilitate hit
identification, hit-to-lead selection, optimize the absorption, distribution, metabolism,
excretion and toxicity profile and avoid safety issues.
The development of any potential drug begins with years of scientific study to determine the
biochemistry behind a disease, for which pharmaceutical intervention is possible. The result
is the determination of specific receptors (target). In the modern era, computer-aided drug
design (CADD) has considerably extended its range of applications, spanning almost all
stages in the drug discovery pipeline, from target identification to lead discovery, from lead
optimization to preclinical or clinical trials.
Drug researchers using structure-based design benefit from a new process of visualizing and
modeling promising compounds at the molecular level. It can facilitate the acquisition and
application of knowledge, improve the quality and currency of knowledge and business

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processes in all areas of business as well as in medical research. In drug discovery process, it
can assist in building hypotheses about desirable chemical properties when designing the
drugs, to refine and modify drugs candidates. Compound databases provide the psycho-
chemical structural data for computational drug discovery method used in component
screening and profiling. Briefly, the IT plays an important role in drug discovery process by :
(i) Computer – analyzing molecular structure
(ii) Databases – organizing data about specific molecules and compounds.
(iii)Software‟s – visualizing and modeling molecules
CONCLUSION
In recent years, computational drug design and more specifically virtual screening, has
emerged as a powerful tool in drug discovery. There are numerous approaches to drug design
depending on the types of information available about the bioactive „ligands‟ and the
therapeutic protein target.