To understand the prospects of graphene nanomaterials in studying complex biomolecular systems, we performed molecular docking and molecular dynamics simulations of the interaction of the drug, pyrazinamide (PZA) and PZA-functionalized graphene with the pncA enzyme. Docking simulations predict the plausible binding mode of the graphene/PZA system with the pncA protein and advocate that PZA functionalized onto graphene facilitates target-specific binding of PZA within the protein following a lock and key mechanism. In the absence of PZA, graphene exhibits enhanced attractive interaction with adjoining amino acid residues along the binding pathway, demonstrating a significant extent of rippling within the sheet. The simulations highlight the fact that the presence of graphene arrests the free rattling movement of PZA around the binding pocket of the protein, thereby improving specificity towards targeting. Interestingly, no major structural deformation in protein was induced by the presence of graphene, and the interaction between ligand and receptor is mainly hydrophobic in nature. The energetics of interaction demonstrates that non-covalent van der Waals and Coulombic forces play the foremost role in the binding of PZA with the pncA protein.