Gas chromatography-mass spectrometry analysis in vitro antibacterial efficacy and in silico molecular docking of compounds produced by endophytes isplated from indegenous medical plants.

Abstract

Native medicinal plants have been traditionally used to treat various bacterial infections, fungal infections, cancers, viral infections and cardiovascular diseases. Endophytic bacteria residing inside the tissues of traditional medicinal plants are capable of producing the therapeutically important bioactive compounds. The bioactive compounds can be used as alternative therapeutic agents thus helping to combat antimicrobial resistance in pathogenic bacteria. Currently bioactive compounds extracted from endophytic bacteria isolated from medicinal plants native to Zimbabwe has not been evaluated computationally. Therefore, this study aimed to characterise and evaluate the bioactive compounds secreted by endophytes isolated from native Zimbabwe trees for control of clinically important bacteria. Acetone, methanol and ethyl acetate extracts from 24 endophytes were evaluated for antimicrobial efficacy against Escherichia coli and Staphylococcus aureus by agar well diffusion assay. Total genomic DNA was extracted from the endophytic samples expressing potent antimicrobial activity. Amplification of 16 S rRNA gene was used to confirm that the endophytic isolated are bacteria. Amplification of RAPDs using the M13 forward primer was used to differentiate the endophytic bacteria. Gas chromatography-mass spectrometry (GC-MS) was used to identify the endophytic compounds present in the extracts and a SwissADME online tool was used to evaluate the pharmacokinetic properties of the most abundant endophytic compounds. The bioactivityspectrum of the selected endophytic compounds was predicted by a PASSonline tool. Potential bacteria protein targets namely lumazine synthase, tryptophan synthase subunit beta and UDPN acetylglucosamine 1-carboxyvinyltransfrase were selected for molecular docking to evaluate the specificity and affinity of the selected endophytic compounds to the potential drug targets. M13 RAPDs analysis indicated that the endophytic bacteria are not the same. Endophytic acetone extracts from sample 1, 3, 9 and 17 exhibited the strongest antimicrobial efficacy against E. coli and S. aureus. Sulfonamide derivates, pyrazolo (3,4-d) pyrimidine derivatives, indolizine derivatives, quinone derivatives, furan derivatives, organic acids, fused uracils, aroma compounds and phenolic compounds were identified by gas chromatography-mass. The diverse compounds identified by GC-MS could be responsible for potent antimicrobial activity against E. coli and S. aureus. Predicted solubility of the endophytic compounds ranged from soluble to very soluble in water, with only eicosane, 2-(1-Fluorovinyl)-5-nitropyridine, octadecane and hexadecane displaying poor solubility. Most of the abundant endophytic compounds satisfied the Lipinski's rule of five. Compounds that had predicted function of phobic treatment were all predicted to cross the blood-brain barrier. 3-Amino-2,2,4-trimethylhexane, octadecane, 2-(1H-Imidazol-2-yl)acetic acid, 2-Piperidinone and 5H,10H-Dipyrrolo[1,2-a:1',2'-d]pyrazine-5,10-dione, octahydro-, (5aS,10aS)- were the most abundant endophytic compounds in all endophytic samples and were selected for in silico molecular docking against potential antibacterial drug targets namely lumazine synthase, tryptophan synthase and UDPN acetylglucosamine 1-carboxyvinyltransfrase. Prediction of bioactivity spectrum of 3-Amino-2,2,4-trimethylhexane, octadecane, 2-(1H-Imidazol-2-yl)acetic acid, 2-Piperidinone and 5H,10H-Dipyrrolo[1,2-a:1',2'-d]pyrazine-5,10-dione, octahydro-, (5aS,10aS)- indicated that they have higher chances of exhibiting antimicrobial, and, anticancer and could also be useful in the treatment of phobic disorders. 5H,10H Dipyrrolo[1,2-a:1',2'-d]pyrazine-5,10-dione, octahydro-, (5aS,10aS)- exhibited strong binding affinities to all three potential drug targets. The binding affinity of 5H,10H-Dipyrrolo[1,2-a:1',2'-d]pyrazine-5,10-dione, octahydro-, (5aS,10aS)-is -1.3 kcal/mol was slightly weaker than the binding affinity of ampicillin, when they were docked with lumazine synthase. The analysis of the binding affinities results indicates that 5H,10H-Dipyrrolo[1,2-a:1',2'-d]pyrazine-5,10-dione, octahydro-, (5aS,10aS)- is a potent inhibitor of lumazine synthase and UDP-N acetylglucosamine 1-carboxyvinyltransfrase which are critical for the survival of bacteria. 5H,10H-Dipyrrolo[1,2-a:1',2'-d]pyrazine-5,10-dione, octahydro-, (5aS,10aS)- was selected as lead compound for the development of an antibacterial drug. This study shows the potential of endophytic compounds as drugs scaffolds and can help in combating antibacterial resistance.