Matched molecular pair analysis

Matched molecular pair analysis (MMPA) is a method in cheminformatics that compares the properties of two molecules that differ only by a single chemical transformation, such as the substitution of a hydrogen atom by a chlorine one.

Because the structural difference between the two molecules is small, any experimentally observed change in a physical or biological property between the matched molecular pair can more easily be interpreted.

[1] MMP can be defined as a pair of molecules that differ in only a minor single point change (See Fig 1).

Matched molecular pairs (MMPs) are widely used in medicinal chemistry to study changes in compound properties which includes biological activity, toxicity, environmental hazards and much more, which are associated with well-defined structural modifications.

[citation needed] Analysis of MMPs (matched molecular pair) can be very useful for understanding the mechanism of action.

[citation needed] Activity cliffs are pairs or groups of compounds that are highly similar in the structures but have large different in potency towards the same target.

[7] Activity cliffs received great attention in computational chemistry and drug discovery as they represent a discontinuity in structure-activity relationship (SAR).

The assessment of activity cliffs requires careful consideration of similarity and potency difference criteria.

[13][14] Beside these, MMPA might pose some limitations in terms of computational resources, especially when dealing with databases of compounds with a large number of breakable bonds.