Antibacterial and antioxidant activities of extracts and isolated compounds from the roots extract of Cucumis prophetarum and in silico study on DNA gyrase and human peroxiredoxin 5

AbstractBackgroundCucumis prophetarumis traditionally used to treat liver and lung disorders, heart failure, diarrhea, gonorrhea, skin infections, intestinal problems and cancer. In the present work, the isolation of two novel compounds along with their antibacterial and antioxidant activities is reported for the first time.MethodsSilica gel column chromatography was applied to separate constituents of the roots ofC. prophetarum.The structures of isolated compounds were established using1H NMR,13C NMR, DEPT-135, COSY, HSQC and HMBC. Agar well diffusion, DPPH assay and ferric thiocyante methods were used for antibacterial, radical scavenging and anti-lipid peroxidation activities, respectively. AutoDock Vina open source program was used for molecular docking analysis.ResultsEvaluation of the in vitro antibacterial activity of the constituents againstS. aureus, B. subtilis, E. coliandS. thyphimuriumrevealed that the hexane extract were active againstE. coliwith IZ of 15.0 ± 1.41 mm, whereas an IZ of 14.6 ± 1.70 mm for MeOH extract was observed againstS. aureus. Compound1displayed IZ of 13.6 ± 0.94 mm againstE. coliand curcurbiatin2showed activity againstB. subtiliswith IZ of 13.3 ± 0.54 mm. The molecular docking analysis showed that cucurbitacins2and3have binding energy of -6.7 and -6.9 kcal/mol, respectively. The methanol and the hexane extracts of the roots ofC. prophetaruminhibited DPPH radical by 70.4 and 63.3% at 100 µg/mL, respectively. On the other hand, the methanol extract inhibited lipid peroxidation by 53.0%.ConclusionThe present study identified five compounds from the root extracts ofC. prophetarum, of which two are novel cucurbitacins (1,2). The in vitro antibacterial activity of the hexane and methanol extracts was better than the activity displayed by the isolated compounds. This is probably due to the synergistic effects of the constituents present in the root extract. The in silico molecular docking study results showed that, compounds2and3have minimum binding energy and have good affinity toward the active pocket, thus, they may be considered as good inhibitor of DNA gyrase B. Furthermore, the “drug-likeness” and ADMET prediction of compounds2–5nearly showed compliance with the Lipinski rule, with good absorption, distribution, metabolism, and excretion generally. The radical scavenging and anti-lipid peroxidation activities of the extracts were better than the isolated compounds. This is attributed to the presence of phenolics and flavonoids as minor constituents in the extracts of these species. Therefore, the in vitro antibacterial activity and molecular docking analysis suggest the potential use of the isolated compounds as medicine which corroborates the traditional use of the roots ofC. prophetarum.