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Objective: The kinetic studies indicate that riboflavin acts as a sensitizer in the photolysis of cyanocobalaminand in this way promotes the degradation of the molecule. Many microorganisms use light for pathogenesis.The present work describes the interaction of vitamin B2 and B12 at molecular level in bacterial enzymeswhich could delineate the possible mechanism of inhibiting the disease producing bacteria. Methodology: The molecular basis of interaction between the flavin derivatives and the B12- dependentenzymes was studied using molecular modeling software, the MVD.. A series of nineteen flavin derivativesand three B12 containing enzymes; glutamate mutase, diol dehydratase and methionine synthase were takenfor the study. The potential binding affinity between flavin derivatives and B12 enzymes was checked on thebasis of lowest docking score, number of hydrogen bonds and favorable binding modes. Results: We found riboflavin, 2-ketoflavin and 4-ketoflavin as the best interacting compounds with each ofthe three enzymes taken. The regions containing lone pair of electrons are critical for the maximum numberof binding conformations. Conclusion: It may be concluded that flavin derivatives may influence the activity of B12 enzymes. Therefore,the understanding of molecular basis of this interaction and the identification of the key factors involved,might be useful to design new molecules with enhanced selectivity towards B12 dependent enzymes. Thiscan lead to the screening and discovery of new compounds as useful antibiotics and the active natural drugs.