Chapter 3: Small molecules and disease

Abstract

"Big" molecules such as proteins and genes still continue to capture the imagination of most biologists, biochemists and bioinformaticians. "Small" molecules, on the other hand, are the molecules that most biologists, biochemists and bioinformaticians prefer to ignore. However, it is becoming increasingly apparent that small molecules such as amino acids, lipids and sugars play a far more important role in all aspects of disease etiology and disease treatment than we realized. This particular chapter focuses on an emerging field of bioinformatics called "chemical bioinformatics"--a discipline that has evolved to help address the blended chemical and molecular biological needs of toxicogenomics, pharmacogenomics, metabolomics and systems biology. In the following pages we will cover several topics related to chemical bioinformatics. First, a brief overview of some of the most important or useful chemical bioinformatic resources will be given. Second, a more detailed overview will be given on those particular resources that allow researchers to connect small molecules to diseases. This section will focus on describing a number of recently developed databases or knowledgebases that explicitly relate small molecules--either as the treatment, symptom or cause--to disease. Finally a short discussion will be provided on newly emerging software tools that exploit these databases as a means to discover new biomarkers or even new treatments for disease.

Figure 1. A pathway diagram for Phenylketonuria as taken from SMPDB (http://www.smpdb.ca).

Figure 2. A screenshot montage illustrating the types of viewing and searching options available in HMDB (http://www.hmdb.ca).

Figure 3. A screen shot of DrugBank's SNP-ADR table.

This displays the information on the adverse drug reactions (ADRs) and associated SNP (single nucleotide polymorphisms) with certain drugs and drug targets (http://www.drugbank.ca).

Figure 4. A screenshot montage illustrating the types of viewing and searching options available in T3DB (http://www.t3db.org).