De-Novo Design of Hits Against New Delhi Metallo-β-Lactamase Enzyme

De-Novo Design of Hits Against New Delhi Metallo-β-Lactamase Enzyme

Arindam Maity, Sarmi Sardar, Shilpa Chatterjee, Nripendra Nath Bala, Sudhan Debnath, Debanjan Sen
Copyright: © 2022 |Pages: 13
DOI: 10.4018/IJQSPR.290010
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Abstract

The New Delhi Metallo-β-lactamase 1 (NDM-1) is a class of Metallo-β lactamase enzyme. It is responsible for hydrolyzing almost all β-lactam antibiotics, leading to multi-drug resistance in bacteria. The lack of specific therapeutic options against this target creates an emerging need to develop new molecules against it. The multistep fragment- and knowledge-based de-novo design methods were considered for this study to design small molecules. The designed molecules were evaluated by molecular docking and dynamics simulation, followed by drug-likeness prediction. This study reports that a new drug-like chemical entity exhibits good binding behavior against the MDM-1 enzyme. Nonetheless, in-depth biological evaluation is required to determine the efficacy of the designed binders to develop new therapeutics against NDM-1.
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2. Material And Methods

All computational work was conducted using the computer consisting intel i9 9900k processor integrated with RTX 2070 NVIDIA GPU, running over Linuxmint 19.3 operating system. Opensource PyMOLTM 1.8.4.0, Free Maestro virtualizer was used to virtualize the 3D structures. The Openbabel software (O’Boyle et al., 2011) was used to generate requires ligand file format. Charm-Gui ligand designer (Lee & Im, 2019) (https://molsoft.com/mprop/) online server software was used to perform drug-likeness property prediction respectively.

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