Molecular Design

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INDUSTRY SNAPSHOT

Molecular design is a big bag of tricks comprised of the principles of biochemistry, medicinal chemistry, molecular biology, and computerized molecular modeling, with a pinch of mathematics and computer science thrown in for good measure, aimed at isolating a novel chemical compound, assessing its beneficial uses, and finding a means to synthesize it in a form optimal to the target use. Enormous advances in high-performance computing and visualization techniques have pushed molecular design to the forefront of biotechnology research. In place of random laboratory screening of chemical compounds, molecular design uses computational chemistry to produce research chemicals aimed at synthesizing new compounds for employment in a commercial market. The leading companies in the pharmaceutical, chemical, and agribusiness industries all make use of molecular design for integration into new products.

Molecular design greatly streamlines the painstaking and time-consuming process of weeding through enormous chemical "libraries" to find molecules appropriate for a specific application, a process that requires screening molecules one at a time. Scientists are now able to cut their time and effort considerably by using molecular design screening processes to isolate in minutes the precise chemical compounds that interact appropriately with their target. Meanwhile, software tailored to the process is employed to create a simulation of the chemical compound's action in its target situation, be it a pharmaceutical medicine or an agricultural crop. Molecular design allows many of these advances to take place through genetic research. This is an area of rapidly increasing importance in medicine and industry, in part because extraordinary advances in computing make it possible to conduct accurate theoretical and experimental studies of enzymes, nucleic acids, and bio-molecular assemblies.

ORGANIZATION AND STRUCTURE

Biological activity is dependent on the three-dimensional geometry of specific functional groups. Biomolecular research has traditionally required synthesis and screening of large numbers of molecules to produce optimal activity profiles, producing an average of one compound a week. Combinatorial chemistry allows researchers to amass libraries of large populations of molecules (100,000 in a matter of weeks) for screening compounds. Similarly, advancements of modern computers, which have become fast, small, and affordable, allow researchers to visualize molecular structure and activity on screen rather than in a test tube. Moreover, advances in chemical models and program interfaces allow researchers to describe the mechanisms of biomolecular activity. Finally, high throughput robotic screens identify which compounds exhibit desired activity against the target. These potential lead candidates are then sold or licensed as information to the subsequent biotech companies for further product development and marketing in the individual sectors.

While computers allow the visualization of chemical interactions and large information databases, they have not entirely replaced experimentation in the lab. The final key to the technology that has made possible the massive libraries of potentially profitable biotech molecules each year is the process of combinatorial chemistry. First developed as a scheme to save time in drug research, the approach has evolved into the ability to create large numbers of organic compounds with the ability to tag them in such a way that those with optimal properties can be screened and identified. Combinatorial chemistry has reduced the time required to profile an optimum form of the compound from years to weeks.

College and university departments and institutes traditionally account for the majority of molecular design and research, although successful business applications had attracted a tremendous amount of attention by the middle years of the first decade of the 2000s and have enabled industry growth. The genetic engineering sector is responsible for much of this attention, with its promise of powerful new super drugs and boosted agricultural yields, although the latter generated a storm of controversy in the late 1990s (Also see the essay entitled Genetic Engineering). Major changes in molecular design technique have enabled numerous small research companies to operate with specialized core technologies and computer programs. Design companies then lease their software and technology. Alternately, they can carry out the molecular design that fuels the rest of the industry, working closely with international pharmaceutical companies.

Within the molecular design industry, individual molecular design companies tend to center on a patented specialized technology that can speed the search for compounds with properties that react favorably with a desired target. Once fully established, large corporations often acquire all or part of the smaller companies and their discovery processes.

The discovery and analysis of genes and their manifestations has come to be known as genomics. Coupled with other major technological advances in molecular design, the use of genomics to identify molecular targets revolutionized the molecular design industry in the 1990s. Giant undertakings, such as the Human Genome Project, offer an abundance of information accessible on highly sophisticated computerized databases. Having identified the biological target—an enzyme, hormone, growth factor, or other protein—the researcher has a point of entry for chemical manipulation.

Efficient and productive realization of molecular design techniques allows the biotech industry to profit from small molecule development and discovery in each of these areas. The pharmaceutical industry entirely depends upon the discovery and selective development of molecules possessing characteristics that may become profitable drugs. In...