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. 2021 Sep 1;10(9):1062.
doi: 10.3390/antibiotics10091062.

Syzygium aromaticum Extracts as a Potential Antibacterial Inhibitors against Clinical Isolates of Acinetobacter baumannii: An In-Silico-Supported In-Vitro Study

Abdelhamed Mahmoud  1 , Magdy M Afifi  1 , Fareed El Shenawy  1 , Wesam Salem  2 , Basem H Elesawy  3
Affiliations

Syzygium aromaticum Extracts as a Potential Antibacterial Inhibitors against Clinical Isolates of Acinetobacter baumannii: An In-Silico-Supported In-Vitro Study

Abdelhamed Mahmoud et al. Antibiotics (Basel). .

Abstract

Imipenem is the most efficient antibiotic against Acinetobacter baumannii infection, but new research has shown that the organism has also developed resistance to this agent. A. baumannii isolates from a total of 110 clinical samples were identified by multiplex PCR. The antibacterial activity of Syzygium aromaticum multiple extracts was assessed following the GC-Mass spectra analysis. The molecular docking study was performed to investigate the binding mode of interactions of guanosine (Ethanolic extract compound) against Penicillin- binding proteins 1 and 3 of A. baumannii. Ten isolates of A. baumannii were confirmed to carry recA and iutA genes. Isolates were multidrug-resistant containing blaTEM and BlaSHV. The concentrations (0.04 to 0.125 mg mL-1) of S. aromaticum ethanolic extract were very promising against A. baumannii isolates. Even though imipenem (0.02 mg mL-1) individually showed a great bactericidal efficacy against all isolates, the in-silico study of guanosine, apioline, eugenol, and elemicin showed acceptable fitting to the binding site of the A. baumannii PBP1 and/or PBP3 with highest binding energy for guanosine between -7.1 and -8.1 kcal/mol respectively. Moreover, it formed π-stacked interactions with the residue ARG76 at 4.14 and 5.6, Å respectively. These findings might support the in vitro study and show a substantial increase in binding affinity and enhanced physicochemical characteristics compared to imipenem.

Keywords: GC-Mass; antibiotic-resistant genes; docking; imipenem; penicillin-binding proteins; urine samples; virulence genes; wound swab.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
The incidence of Acinetobacter baumannii isolates among examined clinical samples.
Figure 2
Figure 2
The heat-map illustrates the antibiograms for all the recovered A. baumannii isolates (A1: A10) by ViteK-2 systems. The intensity of colors indicates the numerical value of the MIC (µg/mL). TIC; Ticarcillin: TIM; Ticarcillin/Clavulanic Acid: PIP; Piperacillin; PTZ; Piperacillin/Tazobactam: CTX; Cefotaxime: PM; Cefepime; IPM; Imipenem: MEM; Meropenam: AK; Amikacin: CN; Gentamicin; TOB; Tobramycin: CIP; Ciprofloxacin: Min; Minocycline: CT; Colistin: SXT; Trimethoprim/Sulfamethxazole. Interpretations breakpoint of antibiotic susceptibility is based on CLSI criteria.
Figure 3
Figure 3
1.5% agarose gel electrophoresis of multiplex PCR of virulence and antibiotic resistant genes for the A. baumannii isolates. (A): recA (425 bp) gene for identification A. baumannii. Lane L: Gel pilot 100 bp plus ladder (cat.no. 239045) supplied from QIAGEN (USA) as molecular size DNA marker Lane Pos: Positive control for recA gene confirmed by reference laboratory for quality control. Lane Neg: Negative control. A1 for urine isolates; A5 for wound isolates, A2, A3, A6, A8 for respiratory isolates. (B): iutA (300 bp) virulence gene. (C,D): blaTEM (516 bp) and blaSHV (392 bp) antibiotic resistance genes, respectively.
Figure 4
Figure 4
The differences of MIC and MBC values of Imipenem and S. aromaticum different extracts against A. baumannii isolates. Shown are the medians from at least three independent measurements for MIC (blue) and MBC (yellow). S. aromaticum different extracts (100 mg mL−1) (A): aqueous extract; (B): ethanolic extract; and (C): ethyl acetate extract. Imi: Imipenem (10 mg mL−1). The error bars indicate the interquartile range. Significant differences between the data sets are marked by asterisks (p < 0.05; Kruskal–Wallis test and post hoc Dunn’s multiple comparisons). A1: A8 are the A. baumannii isolates codes. A1: isolates from urine sample; A5: from wound samples; A2, A3, A6, and A8 for respiratory sample.
Figure 5
Figure 5
Molecular interactions of Imipenem with penicillin-binding protein 1 and 3 (PBP1 and PBP3) in Acinetobacter baumannii. Shown are the 2D binding modes upon docking. HBs are represented in blue and green dotted line colors.
Figure 6
Figure 6
Molecular interactions of Guanosine, Apioline, Eugenol, and Elemicin with penicillin-binding protein 1 (PBP1) in Acinetobacter baumannii. Shown are the 3D (left) and 2D (right) binding modes upon docking. HBs are represented in blue and green dotted line colors while π- interactions are shown in yellow.
Figure 7
Figure 7
Molecular interactions of Guanosine, Apioline, Eugenol, and Elemicin with penicillin-binding protein 3 (PBP3) in Acinetobacter baumannii. Shown are the 3D (left) and 2D (right) binding modes upon docking. HBs are represented in blue and green dotted line colors while π- interactions are shown in yellow and orange line colors.
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