Glucosamine-6-phosphate synthase (G6PS) (EC 2.6.1.16), is an one of the drug target for the anti microbial species. Systemic anti bacterial and anti fungal infections are of the growing problems in contemporary medicines, however only limited anti bacterial agents are in clinical practice for selective action with low toxicity. Then there is an emergency need for more effective version of existing molecules as well as new potential target specific molecules. In this scenario, our present study is an attempt to find out specific molecules via in silico screening of novel chalcone based series of compounds targeting the glucosamine-6-phosphate synthase. Among the twenty five novel designed chalcones skeleton series of compounds, all of them have found to be successfully docking inside the active binding domain of G6PS target with a binding energy in a range of -7.35 to -9.99 Kcal/mol with predicted IC50 value range of 4.11 micro molar to 47.68 nano molar respectively.