Muramyl dipeptide is a component of bacterial peptidoglycan, a recognition structure or activator for nucleotide-binding oligomerization domain 2 (NOD2) protein.

[2] Human NOD2 protein of the nucleotide-binding leucine-rich repeat family, is a cytoplasmic receptor involved in host innate immune system defense.

Mutations in the CARD15 gene encoding NOD2 protein have been observed in Crohn's disease patients,[3] decreasing the immune systems of these patients ability to recognize muramyl dipeptide.

Analogues of muramyl dipeptide and their potential for immune response therapies in cancer and disease are being investigated.

[4] Experiments published in 2008 showed that muramyl dipeptide is involved in a molecular pathway in mice that conferred protection from colitis.