Microbial-based natural products as potential inhibitors targeting DNA gyrase B of Mycobacterium tuberculosis: an in silico study

Introduction: Since the emergence of Mycobacterium tuberculosis (MBT) strains resistant to most currently used anti-tubercular drugs, there has been an urgent need to develop efficient drugs capable of modulating new therapeutic targets. Mycobacterial DNA gyrase is an enzyme that plays a crucial role in the replication and transcription of DNA in MBT. Consequently, targeting this enzyme is of particular interest in developing new drugs for the treatment of drug-resistant tuberculosis, including multidrug-resistant tuberculosis (MDR-TB) and extensively drug-resistant tuberculosis (XDR-TB).

Methods: In the present study, multiple computational tools were adopted to screen a microbial-based natural products database (NPAtlas) for potential inhibitors of the ATPase activity of MBT DNA gyrase.

Results and discussion: Twelve hits were initially identified as the top candidates based on their docking scores (ranging from −9.491 to −10.77 kcal/mol) and binding free energies (−60.37 to −73.21 kcal/mol). Following this, computational filters, including ADME-T profiling and pharmacophore modeling, were applied to further refine the selection. As a result, three compounds 1-Hydroxy-D-788-7, Erythrin, and Pyrindolol K2 emerged as the most promising, exhibiting favorable drug-like properties. Notably, 1-Hydroxy-D-788-7, an anthracycline derivative, demonstrated superior binding affinity in molecular dynamics simulations. The RMSD values, ranging from 1.7 to 2.5 Å, alongside RMSF analysis and a detailed evaluation of the established interaction forces, revealed that 1-Hydroxy-D-788-7 was the strongest binder to Mycobacterial DNA Gyrase B. The stable binding and favorable interaction profile highlighted 1-Hydroxy-D-788-7 as a top hit. These comprehensive computational findings strongly support the potential of 1-Hydroxy-D-788-7 as an effective anti-TB lead compound, warranting further experimental validation to confirm its therapeutic efficacy