1. what is hydrophobic effect?

1. what is hydrophobic effect? please provide your answer in thecontext of drug-target intereactions.

2. Discuss thermodynamics of binding (i.e. discuss thermodynamicparameters that affect affinity). How do these parameters areaffected by the hydrophobic effect?

3. suggest an experiment to dissect the contribution of theseparameters and briefly describe it/


1. Hydrophobic effect is influence of non-polar interactionswithin a system or between two systems towards stabilization of thestructure. In the drug-target interactions, the drug is designed inthe fashion wherein, it has hydrophobic groups attached to it,which are attracted towards the target molecules, which are proteinstructures with hydrophobic groups on it.

2. As the hydrophobic interactions between the drug and thetarget improves, the thermodynamic free energy decreases, that isthe system becomes more stable. This shows that the drug is moreeffective in controling the target activity. So, a strongerhydrophobicity in the drug would have better or stronger affinity(defined by strength of hydrophobic interaction) for the target inthe biological system.

3. An experiment to understand this phenomenon can be designed.First the drug is modified to have polar groups on it (lessinteraction with the target). It is fed to the target cells.Indicator is added to study the apoptosis. The results are noteddown of number of cell deaths in a given time. Now the drug withnon-polar groups which can have better hydrophobic interaction withthe target is designed and fed to the cells in the same fashion.The number of cell deaths are noted down in a similar manner. Thenumber of cell deaths are compared with the first experiment whichwould be greater in this case.

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