Discovery of Two Brominated Oxindole Alkaloids as Staphylococcal DNA Gyrase and Pyruvate Kinase Inhibitors via Inverse Virtual Screening

Abstract

In the present study, a small marine-derived natural products library was assessed for antibacterial potential. Among 36 isolated compounds, a number of bis-indole derivatives exhibited growth-inhibitory activity towards Gram-positive strains (Bacillus subtilis and multidrug-resistant Staphylococcus aureus). 5- and 6-trisindoline (5-Tris and 6-Tris) were the most active derivatives (minimum inhibitory concentration, MIC, 4–8 µM) that were subsequently selected for anti-biofilm activity evaluation. Only 5-Tris was able to inhibit the staphylococcal biofilm formation starting at a 5 µM concentration. In order to investigate their possible molecular targets, both natural products were subjected to in silico inverse virtual screening. Among 20 target proteins, DNA gyrase and pyruvate kinase were the most likely to be involved in the observed antibacterial and anti-biofilm activities of both selected natural products. The in vitro validation and in silico binding mode studies revealed that 5-Tris could act as a dual enzyme inhibitor (IC50 11.4 ± 0.03 and 6.6 ± 0.05 µM, respectively), while 6-Tris was a low micromolar gyrase-B inhibitor (IC50 2.1 ± 0.08 µM), indicating that the bromine position plays a crucial role in the determination of the antibacterial lead compound inhibitory activity.

Flavonoids as Potential anti-MRSA Agents through Modulation of PBP2a: A Computational and Experimental Study

“…In silico and in vitro results encouraged us to run an antibiotic synergistic study of these flavonoids with β-lactam antibiotic ampicillin ( Table 2). The result of this study indicated that hesperetin (6), apigenin (4), and chrysin (5) have an additive effect with the β-lactam antibiotic ampicillin (FICI = 1). However, the glycosylated derivatives, rutin (10), diosmin (11)…”

“…On the other hand, the non-glycosylated flavonoids (compounds 1-6) showed interesting fitting inside the PBP2a active site with binding free energy values ranging from −7.0 to −8.0 kcal/mol, while the highly hydroxylated derivative myricetin (1) showed relatively weaker binding affinity (ΔG = −5.8 kcal/mol). Regardless, the convergent binding affinity and interaction modes of the derivatives 1-6 showed different MIC values against MRSA ranged from 15.62 µg/mL for chrysin (5) to 125 µg/mL for myricetin (1) ( Table 2). Being the smallest and the least hydroxylated (i.e., the least hydrophilic) molecule among its counterparts, particularly at ring B, chrysin (5) was able to easily access the PBP2a active site narrow groove during the 20 ns MDS ( Figure 4A,B).…”

“…MIC values were determined for each compound in the library according to the broth microdilution assay [5]. Briefly, test solutions were made by dissolving each tested compound in DMSO (Sigma, Milan, Italy).…”

“…Recently, our research group has initiated an in-silico-based screening campaign to find out new possible drug leads that can be developed into new antimicrobial agents from different natural sources that are still considered the major source of successful antibiotics [5]. Consequently, we decided to continue our in-silico screening using an in-house plant-derived phenolic compounds library.…”

“…(A) Distance changes between the C α atom of residue SER-403 (i.e., the catalytic residue inside PBP2a active site) and compounds 4-6. (B) Snapshots of PBP2a system during the binding process with chrysin(5).…”