Step-by-Step Solution
The addition of hydrophobic constituents, such as methyl group (Me) at the unoccupied position of the structure is carried out in order to fill the available space. This is done to improve the binding interactions of the compounds.
Figure 1 shows addition of methyl group to unoccupied positions at the hydrophobic pockets of structure II.
Such modifications are not carried out earlier because, while designing a lead compound by de novo methods, there has to be some latitude. The methyl groups might interfere with other groups.
This may result in altering the binding interactions of the compound/molecule. This may also lead to no binding. While in that case, there is still a good chance of using an alternative binding mode with different conformational structure of the molecule.
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