The control of beta-lactam antibiotics released through the inhibition of the New Delhi metallo-beta-lactamase 1 (NDM-1) has been identified as a potential target for the treatment of the muti-drugs resistance (MDR) bacteria disease. We have employed molecular dynamics (MD), alanine-scanning mutagenesis and molecular docking techniques to optimize the x-ray NDM-1 structure with 11 drugs (Tigecycline, BAL30072, D-captopril, Penicillin G, Ampicillin, Carbenicillin, Cephalexin, Cefaclor, Nitrocefin, Meropenem, and Imipenem). From our simulations, we found that the 5 residues Asp223, His120, His122, His162 and His189 are responsible for the selectivity of NDM-1 associated drugs.