The Kalimantacin Polyketide Antibiotics Inhibit Fatty Acid Biosynthesis in Staphylococcus aureus by Targeting the Enoyl‐Acyl Carrier Protein Binding Site of FabI

Natural products acting against S. aureus through membrane and cell wall disruption

Covering: 2015 to 2022Staphylococcus aureus (S. aureus) is responsible for several community and hospital-acquired infections with life-threatening complications such as bacteraemia, endocarditis, meningitis, liver abscess, and spinal cord epidural abscess. In recent decades, the abuse and misuse of antibiotics in humans, animals, plants, and fungi and the treatment of nonmicrobial diseases have led to the rapid emergence of multidrug-resistant pathogens. The bacterial wall is a complex structure consisting of the cell membrane, peptidoglycan cell wall, and various associated polymers. The enzymes involved in bacterial cell wall synthesis are established antibiotic targets and continue to be a central focus for antibiotic development. Natural products play a vital role in drug discovery and development. Importantly, natural products provide a starting point for active/lead compounds that sometimes need modification based on structural and biological properties to meet the drug criteria. Notably, microorganisms and plant metabolites have contributed as antibiotics for noninfectious diseases. In this study, we have summarized the recent advances in understanding the activity of the drugs or agents of natural origin that directly inhibit the bacterial membrane, membrane components, and membrane biosynthetic enzymes by targeting membrane-embedded proteins. We also discussed the unique aspects of the active mechanisms of established antibiotics or new agents.

Tackling multidrug-resistant Staphylococcus aureus by natural products and their analogues acting as NorA efflux pump inhibitors

Staphylococcus aureus (S. aureus) is a pathogen responsible for various community and hospital-acquired infections with life-threatening complications like bacteraemia, endocarditis, meningitis, liver abscess, and spinal cord epidural abscess. Antibiotics have been used to treat microbial infections since the introduction of penicillin in 1940. In recent decades, the abuse and misuse of antibiotics in humans, animals, plants, and fungi, including the treatment of non-microbial diseases, have led to the rapid emergence of multidrug-resistant pathogens with increased virulence. Bacteria have developed several complementary mechanisms to avoid the effects of antibiotics. These mechanisms include chemical transformations and enzymatic inactivation of antibiotics, modification of antibiotics' target site, and reduction of intracellular antibiotics concentration by changes in membrane permeability or by the overexpression of efflux pumps (EPs). The strategy to check antibiotic resistance includes synthesis of the antibiotic analogues, or antibiotics are given in combination with the adjuvant. The inhibitors of multidrug EPs are considered promising alternative therapeutic options with the potential to revive the effects of antibiotics and reduce bacterial virulence. Natural products played a vital role in drug discovery and significantly contributed to the area of infectious diseases. Also, natural products provide lead compounds that sometimes need modification based on structural and biological properties to meet the drug criteria. This review discusses natural products and their derived compounds as NorA efflux pump inhibitors (EPIs).

Do Go Chasing Waterfalls: Enoyl Reductase (FabI) in Complex with Inhibitors Stabilizes the Tetrameric Structure and Opens Water Channels

The enzyme enoyl-ACP reductase (FabI) is the limiting step of the membrane's fatty acid biosynthesis in bacteria and a druggable target for novel antibacterial agents. The FabI active form is a homotetramer, which displays the highest affinity to inhibitors. Herein, molecular dynamics studies were carried out using the structure of FabI in complex with known inhibitors to investigate their effects on tetramerization. Our results suggest that multimerization is essential for the integrity of the catalytic site and that inhibitor binding enables the multimerization by stabilizing the substrate binding loop (SBL, L:195-200) coupled with changes in the H4/5 (QR interface). We also observed that AFN-1252 (naphtpyridinone derivative) promotes unique conformational changes affecting monomer-monomer interfaces. These changes are induced by AFN-1252 interaction with key residues in the binding sites (Ala95, Tyr146, and Tyr156). In addition, the analysis of water trajectories indicated that AFN-1252 complexes allow more water molecules to enter the binding site than triclosan and MUT056399 complexes. FabI-AFN-1252 simulations show accumulation of water molecules near the Tyr146/147 pocket, which can become a hotspot to the design of novel FabI inhibitors.

Photocatalytic and antibacterial activity of graphene oxide/cellulose-doped TiO2 quantum dots: in silico molecular docking studies

Graphene oxide (GO) and cellulose nanocrystal (CNC)-doped TiO₂ quantum dots (QDs) were effectively synthesized by employing the co-precipitation method for the degradation of dyes and antimicrobial applications. A series of characterizations, i.e., XRD, FTIR, UV-visible spectroscopy, EDS, FE-SEM, and HR-TEM, was used to characterize the prepared samples. A reduction in PL intensity was observed, while the band gap energy (E _g) decreased from 3.22 to 2.96 eV upon the incorporation of GO/CNC in TiO₂. In the Raman spectra, the D and G bands were detected, indicating the presence of graphene oxide in the composites. Upon doping, the crystallinity of TiO₂ increased. HR-TEM was employed to estimate the interlayer d-spacing of the nanocomposites, which matched well with the XRD data. The photocatalytic potential of the prepared samples was tested against methylene blue, methylene violet, and ciprofloxacin (MB:MV:CF) when exposed to visible light for a certain period. The antibacterial activity of GO/CNC/TiO₂ QDs against Staphylococcus aureus (S. aureus) and Escherichia coli (E. coli) bacteria in vitro was tested to determine their potential for medicinal applications. The molecular docking investigations of CNC-TiO₂ and GO/CNC-doped TiO₂ against DNA gyrase and FabI from E. coli and S. aureus were found to be consistent with the results of the in vitro bactericidal activity test. We believe that the prepared nanocomposites will be highly efficient for wastewater treatment and antimicrobial activities.

Novel prism shaped C3N4-doped Fe@Co3O4 nanocomposites and their dye degradation and bactericidal potential with molecular docking study

Novel prism shaped C₃N₄-doped Fe@Co₃O₄ nanocomposites were fabricated via a co-precipitation route for effective removal of organic pollutants from water and for bactericidal applications. Doping of C₃N₄ in the heterojunction significantly enhanced the photocatalytic and sonocatalytic activity against methylene blue ciprofloxacin (MBCF) dye. The main purpose of doping Fe atoms in the cobalt lattice was to generate crystal and surface defects. Moreover, the optimum doping amount of C₃N₄ for maximum degradation performance was evaluated. A detailed examination of the prepared nanocomposites was carried out systematically using various characterization tools for better understanding. HR-TEM images revealed the formation of novel prism shaped structures that exhibited outstanding degradation of the organic dye in water. Significant bactericidal potential was also observed for the synthesized nanocomposites against Escherichia coli (E. coli) and Staphylococcus aureus (S. aureus) bacteria. In silico, molecular docking studies against β-lactamase, DHFR and FabI enzymes served to elucidate the mechanism governing the bactericidal activity of the as-synthesized nanoparticles (NPs). Furthermore, a scavenging study by DPPH (2,2-diphenyl-1-picrylhydrazyl) assay and COD (chemical oxygen demand) analysis was performed in order to evaluate active species and the anti-oxidant potential of prepared composites.

This study provides new insights into the use of cobalt-based heterojunction photocatalysts for dye degradation and antibacterial applications (a) synthesis mechanism of C₃N₄ (b) schematic of synthesis route adopted for fabrication of nanocomposites.