Understanding how conformational dynamics play a role in metabolic regulation is an important objective in various biological disciplines. Using Molecular Dynamics (MD) simulations, we attempt to elucidate the dynamics involved in regulating two glycolytic enzymes: human liver pyruvate kinase (hL-PYK) and human enolase. Despite being metabolically coupled, both enzymes are regulated quite differently: hL-PYK can undergo allosteric modulation, while enolase is competitively inhibited. In the hL-PYK study, we discern a mechanism of allostery induced by the allosteric activator fructose-1,6-bisphosphate, and the inhibitor alanine. In the case of enolase, previous studies have attempted to make isoform-specific inhibitors of the enzyme; to further explore this objective, we compare the dynamics of two conserved isozymes, enolase 1 and 2, through MD simulations. As a proof of concept, we find compounds that discriminate between the two homologues by performing ensemble virtual screening on MD derived free enolase structures.