Objective: S100 proteins, the low molecular weight calcium binding proteins, have 'EF hand' type conformation. They are identified as markers for various diseases. A member of S100 protein family, S100A9 is involved, in performing important biological functions, by coordinating with S100A8. S100A9 targeted interactions of quinoline-3-carboxamides, differentiates quinoline derivative interaction among varying single point substituents. Inhibition of protein interaction with many important biological markers as RAGE, TLR4/MD2 and others, was accomplished by quinoline-3-carboxamides. Methods: Two quinoline derivatives identified from Toddalia aculeata are analysed for their molecular and ligand properties. Results: Toxicity analysis, show ADMET properties of phytoquinolines, to be supportive. Molecular binding with S100A9 and its heteromer formed with S100A8, are found analogous to binding, with substituted quinoline-3-carboxamides.Among the various ligands used, a phytoquinoline derivative, and methyl substituted quinoline-3-carboxamide, show most stable interactions. Conclusion: This study proposes the use of compounds from source, as potential ligands to target marker S100A9 and its heterodimer.