Unifying Bioinformatics and Chemoinformatics for Drug Design (2011)

Until relatively recently, the field of drug design and development was disconnected from advances in computing and informatics. Without even considering the concept of computing, previous generations of scientists and clinicians had great motivation to examine the symptoms of ill or injured patients, infer from sufficient observation data about the causes of their symptoms, and search for chemical remedies that could cure or somewhat allieviate a person's ailment. Today, remedies come from sources such as herbal medicines, a high-quality nutritional diet, or human-designed medicines developed in research laboratories. However, there are a great number of afflictions where existing natural remedies are insufficient, and intervention using computation can be beneficial. Around the same time the central dogma of molecular biology was proposed in the 1950s, computing technology was being born in vacuum tubes. For the next 10 years, molecular biology and computing each advanced in their own spectacular ways, yet applying computing to problems in molecular biology was still a novelty. By the end of the 1960s, computing had reached a stage mature enough to be applicable to biochemical problems of limited scope, and the first generation of bioinformatics and chemoinformatics was born. Continuing into the next decade, evolutionary trees were one bioinformatics topic Computing technology was slowly becoming a useful tool to explore the theoretical underpinnings of the information representing the mechanisms of life. Both bioinformatics and chemoinformatics have emerged independently in parallel (Jacoby, 2011), much like computing and molecular biology did at first. Their synergy was largely ignored, not for lack of interest, but rather because the computing power necessary to examine and solve large chemical biology problems that impact drug design was still insufficient. (Note the difference between biochemistry, which is biology-centric and focuses on molecule function, versus chemical biology, which focuses on chemical compounds and their biological effects.) Furthermore, from the perspective of pharmaceutical companies, why would they need to consider changing the laboratory techniques which founded their industry in the first place? Fast forward from the 1970s to the present. Over the past decade computing technology has and continues to become cheaper, to the point where it is now possible to 5 www.intechopen.com 2 Bioinformatics equip individual researchers with multi-processor computing workstations that can compute systems applicable to drug design and optimization in a realistic amount of time. With the recent boost in computing power, the era has come where clinicians, wet-lab scientists, and informaticians can collaborate in inter-disciplinary research for the advancement of drug design to improve the quality of life. Clinicians provide tissue samples of patients exhibiting particular symptoms, bench scientists observe tissue behavior and identify critical molecules of interest, and informaticians provide ways to extract information from the tissue sample that can be useful in retroactively understanding the mechanism which brought about the symptoms. However, the power of informatics is not only in its retrospective analysis capability. Depending on the illness or condition under investigation, the objective of a collaborative research project will be for design of a new pharmaceutical, either a retro-active drug (suppress a symptom after it has come about) or a pro-active drug (suppress a symptom before it has come about). Such design is now appreciably impacted by informatics because of the scale of data and precision required for proper understanding of a phenomenon. In this chapter, we provide several examples of this collaborative drug design process that incorporates informatics for chemical biology and their translational experimental impact.