The introduction of The Hitch Hiker’s Guide to the Galaxy begins like this: “Space,” it says, “is big. Really big. You just won’t believe how vastly hugely mindbogglingly big it is. I mean you may think it’s a long way down the road to the chemist, but that’s just peanuts to space. Listen…”
We are becoming used to reading about space exploration, trips to the Moon and Mars, but for scientists, this is not the only space to explore and conquer. Chemistry and biology can be considered as two universes to be explored, the complexity of which has so far only been scratched.
Let’s start with a simple question, how many molecules do we know? Today the chemical compounds synthesized or extracted from natural origin do not exceed 150 million… a huge number at first sight, but if we try to calculate how many molecules we could build using at most 30 atoms choosing between carbon, nitrogen, oxygen, and sulphur, we would get 1060 molecules: a number that written in full would be 1,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000!
No one will have time to synthesize all these compounds, and there would not be enough matter in the universe to create them. So-called drug hunters have always looked for new ways to effectively explore this chemical space to find those molecules that are related to another universe: biological space.
Finding a molecule in the chemical space that is able to act on a specific target is comparable to a search for a needle in the haystack. The dramatic extension of chemical space excludes the use of systematic or random approaches. What is pursued is the so-called rational drug discovery.
Several computational tools are available to identify molecules that play a role in biological space. Among the most recent findings are the efforts of Bajorat from the University of Bonn (Germany) “for the development and application of chemoinformatics and computational chemistry solutions to research problems in medicinal chemistry, chemical biology, and the life sciences.”
In one of his most recent works, he and co-workers analyzed already-known molecules by creating a representation called a chemical space network (CSN) that allows drug hunters to organize and visualize the relationships between chemical structures and their biological activity (structure-activity relationships, SAR). This is not only a depiction of chemical space, but it can be used as a “treasure map” to identify new molecules.
The human genome project has initiated a new era by shifting the focus from DNA to the proteome, the set of all the proteins produced by the human body and necessary for its operation. The 2015 Human Protein Atlas project estimated that approximately 20,000 proteins are encoded from the human genome. The research started from DNA and has become protein orientated because researchers are used to put emphasis on agonist and antagonist of proteins, or receptors and enzymes to understand their usability as therapeutic targets.
The Protein Data Bank is a repository of structural data of biological macromolecules, such as proteins, which were obtained by NMR, x-ray or cryo-electron microscopy (Chemistry Nobel Prize 2017). These data allow us to know the 3D shape of the proteins which is a powerful resource to understand how proteins interact within an organism and use this information. The BioGPS approach is one example where 3D structures of proteins are used to identify which molecules could interact with them, and thus allows navigation in the biological space.
The paradigm for which a molecule acts on a drug “one drug, one target” is, however, a simplistic view of reality. A molecule, or a drug, can act on more proteins and have a much more complex pharmacological effect. We are entering in the pharmacological space, anew universe which is the integration of chemical and biological space… one, two, three spaces to be explored means a very huge amount of “big data” that needs to be analyzed using new algorithms and of new data scientist very well trained in chemistry and biology… a new generation of hitchhiker!
More technically details about how chemical-biology space exploration can be accomplished are described in the article entitled, The hitchhiker’s guide to the chemical-biological galaxy, recently published in the journal Drug Discovery Today. This study was conducted by Giulia Opassi, Alessandro Gesù and Alberto Massarotti from the Department of Pharmaceutical Sciences of the University of Piemonte Orientale.
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