Chemiformatics -  Looking At Small Molecules

Like bioinformatics, cheminformatics is still being defined.    Bioinformatics, in general, is the discipline in which computers are used to store, retrieve, and assist in understanding and making inferences, instead of a text based retrieval system.   Cheminformatics uses chemical structures that researchers provide as input to identify similar compounds that might be screened for biological activity.

The boundary between cheminformatics and bioinformatics is disappearing, but in general it can be said that bioinformatics deals with large molecules such as proteins and nucleic acids, while cheminformatics deals with small molecules that are synthesized in chemical processes, says Phil McHale, Vice President for product marketing at MDL Information Systems.   Bioinformatics blurs into cheminformatics with the processes of target identification, target validation, and assay development.
MDL is a cheminformatics company that enables its customers to store, retrieve, analyze, and make decisions based on chemical structures.   It considers itself to be an ideal position to close the gaps between the large-molecule bioinformatics world and the small-molecule cheminformatics world.

Tripos also considers itself a cheminformatics company, focusing mainly on chemical properties for compounds involved in the early drug discovery and development stages.

Other companies competing in this field include ChemNavigator, and Command Pharmacopeia.  Over the past few years, Pharmacopeia has acquired stable software companies that include a bioinformatics arm, Genetics Computer Group, as well as Molecular Simulations Inc, Synopsis Scientific Systems, and Oxford molecular group. These last two businesses form the cheminformatics part of Pharmacopiea.

ChemNavigator has developed an application that allows researchers to submit a precise structure of comparison with other compounds among the more than 1 million compounds in its library,    President Scott Hutton says that "fuzzy logic" is used to discern chemical similarities between structures.  At ChemNavigator's website, commercially available compounds can be identified, purchased, and delivered to the researcher expeditiously.  According to Hutton, this web-based application research, includes compound background information such as Food and Drug Administration filings, toxicity data, and patent information, helping the researcher to avoid wasting resources on unsuitable candidates.

Anady’s Pharmaceuticals is a young drug discovery company using cheminformatics as a platform on which to bridge the gap between chemistry and biology.  In drug disovery, biology supplies the targets through genomics.   Chemistry provides the compounds to be screened, and assays are developed using biology.  Medicinal chemists take "hints" from those screens and make more compounds to be tested by biologists in animals.  It is essential to tie these processes together using informatics.
Anady’s is developing an integrated cheminformatics management system to inventory compound libraries, analyze the libraries for specific chemical and drug like properties, store results from high-throughput screening, and predict new chemical structures, says Kleanthis G Xanthopoulos, President and CEO.  Once these compounds are identified, Anady’s medicinal chemists synthesise these materials.  In effect, Anady’s uses cheminformatics software to prescreen compounds to identify more active drug-like compounds.

The search for new drugs cannot be done randomly given the enormous number of possibilities, so computer algorithms are critical for efficiently screening for biologically active structures,   Xanthopoulos says.   Once these drugs are identified, Anady’s medicinal chemists synthesize them in small amounts for experimental screening.  Once a small-molecule drug is in the lab, it can be modified as necessary to match the requirements of drug application.   Anady’s research is primarily
in what it calls riboproteomics, the study of RNA-protein interactions.

Many bioinformatics companies are following courses that blur bioinformatics into cheminformatics.  For example, Viaken out sources standard software products for companies in life sciences industry.  But over the past year, the company has expanded into chemical properties and structures in order to extend the range and depth of what it can do for its customers, says Steve Gardner, Viakens Vice President and Chief Technical Officer.