Novel Bacterial Topoisomerase Inhibitors Exploit Asp83 and the Intrinsic Flexibility of the DNA Gyrase Binding Site

Abstract

DNA gyrases are enzymes that control the topology of DNA in bacteria cells. This is a vital function for bacteria. For this reason, DNA gyrases are targeted by widely used antibiotics such as quinolones. Recently, structural and biochemical investigations identified a new class of DNA gyrase inhibitors called NBTIs (i.e., novel bacterial topoisomerase inhibitors). NBTIs are particularly promising because they are active against multi-drug resistant bacteria, an alarming clinical issue. Structural data recently demonstrated that these NBTIs bind tightly to a newly identified pocket at the dimer interface of the DNA–protein complex. In the present study, we used molecular dynamics (MD) simulations and docking calculations to shed new light on the binding of NBTIs to this site. Interestingly, our MD simulations demonstrate the intrinsic flexibility of this binding site, which allows the pocket to adapt its conformation and form optimal interactions with the ligand. In particular, we examined two ligands, AM8085 and AM8191, which induced a repositioning of a key aspartate (Asp83B), whose side chain can rotate within the binding site. The conformational rearrangement of Asp83B allows the formation of a newly identified H-bond interaction with an NH on the bound NBTI, which seems important for the binding of NBTIs having such functionality. We validated these findings through docking calculations using an extended set of cognate oxabicyclooctane-linked NBTIs derivatives (~150, in total), screened against multiple target conformations. The newly identified H-bond interaction significantly improves the docking enrichment. These insights could be helpful for future virtual screening campaigns against DNA gyrase.

Antioxidant, Anti-Lung Cancer, and Anti-Bacterial Activities of Toxicodendron vernicifluum

“…The in vitro, in vivo, and computational studies indicated that the antibacterial activity of MBE was due to the synergism of various compounds present in the MBE. The growth of bacterial pathogens can be inhibited through targeting of the growth and virulence protein topoisomerases II, IV, and DNA [23] as the new DNA gyrase inhibitor NBTIs is a potential target [24]. There are several works that indicate that targeting the NBTIs can be an excellent strategy for the development of a novel antibacterial agent [25,26,27] against MRSA [28].…”

“…A computational approach was applied to screen and predict the underlying mechanism of the potent activity of the MBE based on the GC-MS data. For the in silico antibacterial activity two important bacterial protein targets, PBP2a protein from MRSA (PDB ID:3ZFZ) [47] and novel bacterial topoisomerases inhibitors (PDB ID:4PLB) [24], and for the anti-lung cancer activity, anti-pro-apoptosis protein survivin (PDB ID: 1F3H) [21], were retrieved from the RCSB protein data bank (PDB) (). Next, the structure of the compounds from the MBE detected by GCMS was generated based on canonical SMILES (Simplified Molecular Input Line Entry System) () using the ACD/ChemSketch.…”

“…DNA gyrase is involved in the manipulation of the topological state of the bacterial DNA, which is also essential for the survival of the bacteria [23]. New DNA gyrase inhibitors called novel bacterial topoisomerases inhibitors (NBTIs) is a potential target to inhibit the DNA gyrase expression [24]. There are several research findings which indicate the application of the NBTIs on the development of novel antibacterial agents [25,26,27].…”

Bioactive Potential of 2-Methoxy-4-vinylphenol and Benzofuran from Brassica oleracea L. var. capitate f, rubra (Red Cabbage) on Oxidative and Microbiological Stability of Beef Meat

“…An in silico docking study was applied to investigate the interactions between the compounds, from the cabbage extracts and two target bacterial proteins (lipoprotein; LpxC and bacterial type II topoisomerase inhibitor; NBTI). The crystal structure of bacterial targets proteins such as LpxC (PDB ID: 3U1Y) UDP-3-O-(R-3-hydroxymyristoyl)-N-acetylglucosamine deacetylases, and novel bacterial topoisomerases inhibitors (PDB ID: 4PLB) [9] were obtained from the protein data bank (https://www.rcsb.org/). The compound (ligands) structure was prepared using the ACD/ChemSketch based on the canonical SMILES procured from NCBI (https://www.ncbi.nlm.nih.gov/pccompound).…”

“…The molecular interactions results indicated that among the tested compounds, benzofuran and 2-Methoxy-4-vinylphenol showed the higher negative docking score against 4PLB (−8.229 Kcal.mol −1 ) and LpxC (−8.63 Kcal.mol −1 ), respectively (Table 3). LpxC, an emerging target in Gram-negative bacteria, leads to the synthesis of Lipid A biosynthetic pathway, which is an essential component for the survival of bacteria [9]. In addition, it makes it resistant to commonly used antibiotics [26].…”