Screening Commercial Compounds When Creating Novel Drugs
Can the drugs of the future be found in commercial space? The size of the drug-like chemical space has been estimated be around 1063 molecules. Somewhere in this huge space, we should expect to find the drugs of the future. Aiming to make this space more accessible to scientists, several chemistry vendors have launched commercial databases of drug-like compounds, available off-the-shelf or with a predicted high synthetic availability. Many pharma companies are also launching proprietary databases  (Figure 1).
How to search commercial space When making a virtual screen in chemical space, the scientists usually starts with a template, being a reference compound or a hit from a screen. One of the fastest way to screen large databases is via fingerprint methods .
When to search commercial space In order to investigate what kind of molecules can be found in commercial space, we have run fingerprint-based similarity searches for leads, drugs and their analogues in 10 different small molecule drug discovery projects . The results show that the highest similarity scores and the highest number of analogues are found for less decorated templates (Figure 2). This applies to both lead-like and drug-like compounds. Examples of templates and hits are shown in Figure 3.