The students usually complete three puzzles of increasing difficulty during this outreach activity.  Each puzzle is followed by a discussion to emphasize one of the goals of the lesson.

Demonstration Flowchart


The Allegra puzzle is a particularly good example to employ at the beginning of the demonstration.  The students will often be familiar with Allegra either through personal use or through exposure via television commercials.  In addition, this particular puzzle introduces the concept that during the game a molecular fragment (in this case the blue benzene ring) may be used more than once in the solution.   Most importantly, since there are only three scaffold blanks to fill and three pieces to select from and since Allegra has an axis of symmetry, the solution is easily achieved.  Mathematically, a scaffold with three Velcro blanks coupled with three possible pieces can create 27 (33; 3 X 3 X 3) possible molecules.  The equivalence of scaffold slots 1 and 2 in the Allegra example simplifies the discovery of the solution even further so that there are 18 possible answers.  This simple type of puzzle works well for starting the game since students can usually find the correct answer within approximately three to five iterations (about five minutes of game play).

After completion of the first puzzle, Allegra, it is explained to the students that drugs are usually discovered through an interactive exchange between chemists and biologists.  Optimization of an initial hit structure follows a trial and error path where chemists submit compounds for biological testing in a similar manner to the game being played.  The biologist uses an assay to determine the potency of the compound and feeds that data back to the chemist.  With this information, the chemist can redesign the molecule to hopefully synthesize a more potent molecule for a second round of testing.  This cycle of “synthesis followed by assay” continues until the optimal compound is obtained as an effective treatment for the disease.

The shape of Allegra is discussed and the role that molecular structure plays on the observed biological activity is emphasized during this discussion.  It is pointed out that the molecular structure dictates the activity of the pharmaceutical.  The shape of the molecule allows it to fit well into the biological target protein.  Depending on the level of the student, a discussion can also be initiated regarding the types of atoms in the molecule or the functional groups present.  Hence, the game affords the students an opportunity to interact with functional groups as they manipulate the game pieces.  Other tools utilized by medicinal chemists such as X-ray crystallography and structural based design can also be discussed.


A second more difficult puzzle, Amoxicillin, is played next.   Again a scaffold containing three Velcro blanks is employed, but six possible molecular pieces are given out: three that are in the solution and three that are not.  The number of combinations for this puzzle is 216 (63; 6 X 6 X 6).  After completion of the second, more difficult puzzle, the students are prepared for a discussion of the mathematics behind the difficulty of the puzzles.  The number of combinations is dictated by the number of pieces and the number of empty slots on the scaffold.  The formula for the number of combinations is the number of molecular pieces to the power of the number of Velcro blanks.

Once the students understand the limited number of combinations possible in their puzzles, a discussion of the enormous mathematical possibilities facing the medicinal chemist commences.   It has been estimated1 that the possible number of drug-like molecules is somewhere between 1023 and 10180 with the number 1060 often quoted in the literature.2  Students are usually amazed by the magnitude of the problem facing the medicinal chemist at this point since the puzzles they are struggling with have so few possible solutions in comparison to this large number.


Usually, the demonstration ends with a puzzle of higher complexity.  The Lipitor (atorvastatin) puzzle, is an example with this level of difficulty (625 combinations possible – 54; 5 X 5 X 5 X 5).

After the students solve the most difficult puzzle, a discussion of the cost of drug research begins.  Students are asked to review the amount of play money they have at the end of the game and to consider the cumulative cost of each step along the path of developing a new pharmaceutical.  It is explained that the game the students have played mimics only the early stage of drug research.   The later steps in drug development are described including animal testing, pre-clinical toxicology, and the three main phases of human clinical trials.  The accumulated expenditure of each step of the development pathway leads to a current estimate of the cost to bring a new pharmaceutical to market of $2.56 billion.4



(1)  Polishchuk, P. G.; Madzhidov, T. I.; Varnek, A. Estimation of the Size of Drug-like Chemical Space Based on GDB-17 Data.  J. Comput. Aided Mol. Des. 2013, 27, 675-679. 

(2)  Bohacek, R. S.; McMartin, C.; Guida, W. C. The Art and Practice of Structure-Based Drug Design: A Molecular Modeling Perspective. Med. Res. Rev 1996, 16, 3–50.

(3) Hay, M.; Thomas, D. W.; Craighead, J. L.; Economides, C.; Rosenthal, J. Clinical Development Success Rates for Investigational Drugs.  Nature Biotechnology 2014, 32, 40-51.

(4)  DiMasi, J. A., Grabowski, H. G., Hansen, R. Innovation in the Pharmaceutical Industry: New Estimates of R&D Costs. J. Health Econ. 2016, 47, 20-33.