In silico Analysis of Phytocompounds from Plumbago auriculata, Gymnema sylvestre, and Andrographis paniculata as Potential Inhibitors of NDM-1 in Klebsiella pneumoniae

^1,6 Department of Physics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand.
² Department of Biochemistry, Oriental Institute of Science and Technology, Bardhaman, West Bengal, 713102, India.
³ Department of Microbiology, Raiganj University, Raiganj, West Bengal - 733143, India.
⁴ Department of Microbiology, Faculty of Science, Assam down town University, Guwahati, 781026, India
⁵ Department of Medical Laboratory Science, Regional Institute of Paramedical and Nursing Sciences, Aizawl, 796017, India

Published online: 21 January 2026

Abstract

New Delhi metallo-β-lactamase-1 (NDM-1) is a major determinant of antibiotic resistance responsible for hydrolyzing β-lactam antibiotics, including carbapenems, in Klebsiella pneumoniae. This study aimed to find potential phytocompound inhibitors of NDM-1 from three medicinal plants, Andrographis paniculata, Gymnema sylvestre, and Plumbago auriculata, by using an in silico computational approach. The NDM-1 three-dimensional structure was obtained from the Protein Data Bank, and phytocompound structures were collected from the IMPPAT database. AutoDock Vina has been used for performing molecular docking, followed by visualization and interaction analysis using AutoDock Tools 1.5.7. Pharmacokinetic and toxicity screening (ADMET and ProTox-III) was performed to assess drug likeness and safety. Docking results revealed different inhibitory potentials among screened phytocompounds. Alpha-Amyrin from Plumbago auriculata shows the highest binding affinity (-8.9 kcal/mol), followed by Beta-Amyrin from Gymnema sylvestre and Plumbago auriculata (-8.8 kcal/mol). All selected phytocompounds showed favourable ADMET profiles and low predicted toxicity, with Beta-Amyrin, Alpha-Amyrin, Daucosterol, and Resiniferonol showing the safest toxicity scores. These findings suggest that selected phytocompounds, particularly Alpha-Amyrin and Beta-Amyrin, may provide promising lead compounds for developing NDM-1 enzyme inhibitors. Despite this, further in vitro and in vivo validation is required to confirm their therapeutic potential.