Abstract
Topoisomerases are important targets for antibacterial and anticancer therapies. Bacterial topoisomerase I remains to be exploited for antibiotics that can be used in the clinic. Inhibitors of bacterial topoisomerase I may provide leads for novel antibacterial drugs against pathogens resistant to current antibiotics. TB is the leading infectious cause of death worldwide, and new TB drugs against an alternative target are urgently needed to overcome multi-drug resistance. Mycobacterium tuberculosis topoisomerase I (MtbTopI) has been validated genetically and chemically as a TB drug target. Here we conducted in silico screening targeting an active site pocket of MtbTopI. The top hits were assayed for inhibition of MtbTopI activity. The shared structural motif found in the active hits was utilized in a second round of in silico screening and in vitro assays, yielding selective inhibitors of MtbTopI with IC50s as low as 2 µM. Growth inhibition of Mycobacterium smegmatis by these compounds in combination with an efflux pump inhibitor was diminished by the overexpression of recombinant MtbTopI. This work demonstrates that in silico screening can be utilized to discover new bacterial topoisomerase I inhibitors, and identifies a novel structural motif which could be explored further for finding selective bacterial topoisomerase I inhibitors.
Highlights
Antibiotic resistance is a dire problem that is facing the global community
The molecular dynamics (MD)-generated structures opened the DNA-binding pocket and allowed the compounds to bind much deeper inside the pocket, as opposed to binding closer to the surface on the 5D5H crystal structure (Fig. 1)
There is an urgent need for new TB drugs, preferably via a novel mechanism
Summary
Antibiotic resistance is a dire problem that is facing the global community. The emergence of drug-resistant strains of pathogenic bacteria is rendering our current antibiotics almost powerless in certain cases[1,2], and this has grave implications for the future of public health. Loss of TopI activity in M. tuberculosis leads to cell death For these reasons, bacterial topoisomerase I is a promising new drug target, especially in mycobacteria. Bacterial topoisomerase I is a promising new drug target, especially in mycobacteria When it comes to drug discovery, there are many valid approaches including virtual docking, high-throughput screening, and fragment-based screening, among others[15,16]. Many programs are available to carry out docking studies, and combined with molecular dynamics, this method can be a powerful tool In these studies, bacterial topoisomerase I was the intended drug target. Bacterial topoisomerase I was the intended drug target In this screen, the crystal structure 5D5H18 for M. tuberculosis TopI (MtbTopI) was used. The in vitro assays results confirmed virtual screening as a worthwhile method of discovering novel bacterial topoisomerase I inhibitors, and identified a novel structural motif as a potential pharmacophore for the inhibition of MtbTopI
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