Evaluation of quercetin as a potential β-lactamase CTX-M-15 inhibitor via the molecular docking, dynamics simulations, and MMGBSA

Antimicrobial resistance (AMR) threatens millions of people around the world and has been declared a global risk by the World Economic Forum. One of the important AMR mechanisms in Enterobacteriaceae is the production of extended-spectrum β-lactamases. The most common ESBL, CTX-M β-lactamases, is spread to the world by CTX-M-15 and CTX-M-14. Sulbactam, clavulanic acid, and tazobactam are first-generation β-lactamase inhibitors and avibactam is a new non-β-lactam β-lactamase inhibitor. We studied that avibactam, sulbactam, clavulanic acid, tazobactam, and quercetin natural flavonoids were docked to target protein CTXM-15. Subsequently, the complexes were simulated using the molecular dynamics simulations method during 100 ns for determining the final binding positions of ligands. Clavulanic acid left CTX-M-15 and other ligands remained in the binding site after the simulation. The estimated binding energies were calculated during 100 ns simulation by the MMGBSA-MMPBSA method. The estimated free binding energies of avibactam, sulbactam, quercetin, tazobactam, and clavulanic acid were sorted as –33.61 kcal/mol, –16.04 kcal/mol, –14 kcal/mol, –12.68 kcal/mol, and –2.95 kcal/mol. As a result of both final binding positions and free binding energy calculations, Quercetin may be evaluated an alternative candidate and a more potent β-lactamases inhibitor for new antimicrobial combinations to CTX-M-15. The results obtained in silico studies are predicted to be a preliminary study for in vitro studies for quercetin and similar bioactive natural compounds. These studies are notable for the discovery of natural compounds that can be used in the treatment of infections caused by β-lactamase-producing pathogens

Combined in silico approach and whole genome sequencing: Acinetobacter baumannii ST218 isolate harboring ADC-73 β-lactamase which has a similar C-loop with ADC-56 and ADC-68 β-lactamase

Purpose: Multidrug-resistant Acinetobacter baumannii is a noteworthy nosocomial-pathogen and these pathogen-borne infections are difficult to treat. It is significant to make strain typing with WGS and to add new genome data to the literature. Therefore, in our study, we aimed to strain typing of the A. baumannii (A24) isolated from Turkey and reveal informations about ADC-73 β-lactamase. Methods: VITEK 2 system was used for the determination of antibiotic susceptibility. WGS was done on the Illumina NovaSeq 6000 platform. WGS results were analyzed with VFDB, ResFinder, PubMLST, IS Finder. Web-based bioinformatics software, homology modelling, molecular docking and dynamics simulations were used to determine all structural information about ADC-73 β-lactamase. Results: A24 was found to be multidrug-resistant. Various virulence factors were found in A24. The sequence type of the isolate was determined as ST218. Genes encoding β-lactamase and aminoglycoside modifying enzymes, and IS elements were present in the genome of A24. Besides, secondary and 3D structures of ADC-73 were analyzed. Following, cefepime and imipenem were docked to ADC-56, ADC-68, and ADC-73 and interactions and stability of substrates were simulated. The binding-energies of imipenem to ADC-68 and ADC-73 were calculated −9.44 and −5.98 kcal/mol, respectively. Likewise, binding-energies of cefepime to ADC-56 and ADC-73 were calculated as −19.84 and −36.54 kcal/mol. Conclusion: A. baumannii ST218 isolate containing ADC-73 was reported for the first time in Turkey by WGS, and the effect of G225S mutation in this β-lactamase on conformational change and possible interactions with cefepime and impinem were investigated in silico

In vitro and in silico evaluation of some plant extracts and phytocompounds against multidrug-resistant Gram-negative bacteria

The spread of multidrug-resistant Gram-negative (MDR) bacteria is a global public health problem, as infections caused by MDR Gram-negative bacteria are difcult to treat. New antibiotic agents need to be developed to overcome this problem, and phytochemicals show promise at this point. In this study, methanol extracts were prepared from cinnamon, thyme, nettle, white tea, rosehip, and antibacterial activity of the methanol extracts was studied against two MDR Gram-Negative bacteria (K. pneumoniae and A. baumannii) by broth microdilution method. The MICs of methanol extracts of cinnamon, rosehip, thyme, white tea for A. baumannii were found as 0.015125 g/ml, 0.07825 g/ml, 0.030625 g/ml, 0.00796875 g/ml, respectively. It was found that only cinnamon methanol extract had antibacterial activity in the used extract concentrations against K. pneumoniae and the MIC value was 0.0605 g/ml. The efects of plant methanol extract with antibacterial activity and imipenem combinations were studied in vitro using the checkerboard method. The FIC Indexes were obtained from the checkerboard results and it was observed that the combination of methanol extract and imipenem showed an antagonistic or additive/indiferent efect but not a synergistic efect. We evaluated the binding afnity of epigallocatechin 3-gallate, quercetin, cinnamaldehyde, carvacrol, and thymol phytocompounds using in silico methods, which are well known as a phytocompounds in white tea, cinnamon, thyme, nettle, and rosehip and have antibacterial activities. The results suggested that these phytocompounds should be supported with in vivo and in vitro experiments to investigate their potential for being inhibitor candidates