Chemical Profile and in-silico Docking Studies on Bioactives from Essential Oil of Cymbopogan pendulus Targeting Penicillin Binding Proteins (PBPs) in Bacteria

Arun Dev Sharma, Inderjeet Kaur

Abstract


Antibiotic resistance in bacteria is the major concern worldwide. PBP (Penicillin binding proteins) have been cited as an appropriate target for therapeutic drug design. In the present study molecular docking followed by wet lab validation was designed to estimate the effect of potent bioactive molecules from Cymbopogan pendulus essential oil against PBP5 protein. GC-FID (gas chromatography with flame-ionization detection) based composition profile, and in-silico docking study was conducted by using CB-dock 2 analysis followed by 2D and 3D interactions. GC-FID revealed Limonene, Neral, Geranial, Linalool, Myrcene as major and minor compounds in Cymbopogan pendulus essential oil. The docking score indicated effective binding of ligands to PBP5. Interactions results indicated that, PBP5/ligand complexes form hydrogen and hydrophobic interactions. Wet lab study validated the anti-bacterial potential of oil against gram-positive and gram-negative bacteria. Therefore, essential oil from Cymbopogan pendulus essential oil may represent potential herbal treatment to mitigate bacterial infections.

Keywords


Bacteria; Docking; lemon grass oil; geranial; Herbal Drug

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References


Apriyanti E, Kurnia D. (2020). Potential of MurA enzyme and GBAP in Fsr quorum sensing system as antibacterial drugs target: In vitro and in silico study of antibacterial compounds from Myrmecodia pendans. Comb. Chem. Highthroughput Screen. 23:1–10.

Barcellos MP, Santos CB, Federico LB, Almeida PF, da Silva CHTP, Taft CA. (2019). Pharmacophore and structure-based drug design, molecular dynamics and admet/tox studies to design novel potential pad4 inhibitors. J Biomol. Struc.Dyn. 37:966–981

Bhatnagar A. (2018). Composition variation of essential oil of Cymbopogon spp. growing in Garhwal region of Uttarakhand, India. J App Nat Sci 10: 363–366.

Brockhurst MA, Harrison F, Veening JW, Harrison E, Blackwell G, Iqbal Z, Maclean C. (2019). Assessing evolutionary risks of resistance for new antimicrobial therapies. Nat. Ecol. Evol. 3: 515–517

Chan LC, Gilbert A, Basuino L, da Costa TM, Hamilton SM, Dos Santos KR, Chambers HF, Chatterjee SS. (2016). PBP 4 Mediates High-Level Resistance to New-Generation Cephalosporins in Staphylococcus aureus. Antimicrob Agents Chemother. 60:3934-41

Chen J.B, Sun S.Q., Tang X.D, Zhang J.Z, Zhou Q. (2016). Direct and simultaneous detection of organic and inorganic ingredients in herbal powder preparations by Fourier transform infrared microspectroscopic imaging. Spectrochimica Acta, 165, 176–182

Chen Y, Zhang W, Shi Q, Hesek D, Lee M, Mobashery S, Shoichet BK. (2009). Crystal structures of penicillin-binding protein 6 from Escherichia coli. J Am Chem Soc. 131:14345-54

Contreras-Martel C, Martins A, Ecobichon C, Trindade DM, Mattei PJ, Hicham S, Hardouin P, Ghachi ME, Boneca IG, Dessen A. (2017). Molecular architecture of the PBP2-MreC core bacterial cell wall synthesis complex. Nat Commun 8: 776-776

da Costa TM, de Oliveira CR, Chambers HF, Chatterjee SS. (2018). PBP4: A New Perspective on Staphylococcus aureus ?-Lactam Resistance. Microorganisms. 22:57.

Fair RJ, Tor Y. (2014). Antibiotics and Bacterial Resistance in the 21st Century. Perspect. Medicin. Chem.6: S14459

Gartika M, Pramesti HT. (2018). A terpenoid isolated from sarang semut (Myrmecodia pendans) bulb and its potential for the inhibition and eradication of Streptococcus mutans biofilm. BMC Complement. Altern. Med.18:1–8

Kurnia D, Apriyanti E. (2019). Antibacterial flavonoids against oral bacteria of Enterococcus faecalis ATCC 29212 from Sarang Semut (Myrmecodia pendans) and its inhibitor activity against enzyme MurA. Curr. Drug Discov. Technol.16:290–296

Lima SL, Colombo AL and de Almeida Junior JN. (2019). Fungal Cell Wall: Emerging Antifungals and Drug Resistance. Front. Microbiol. 10:2573

Lu Z, Wang H, Zhang A, Liu X, Zhou W, Yang C, Guddat L, Yang H, Schofield CJ, Rao Z. (2020). Structures ofMycobacterium tuberculosisPenicillin-Binding Protein 3 in Complex with Fivebeta-Lactam Antibiotics Reveal Mechanism of Inactivation. Mol Pharmacol 97: 287-294

Mancianti, F., Valentina, V. (2020). Biological Activity of Essential Oils" Molecules 25: no. 3: 678.

Masters EA, de Mesy Bentley KL, Gill AL, Hao SP, Galloway CA, Salminen AT (2020). Identification of Penicillin Binding Protein 4 (PBP4) as a critical factor for Staphylococcus aureus bone invasion during osteomyelitis in mice. PLoS Pathog 16(10): e1008988

Moon TM, D'Andréa ÉD, Lee CW, Soares A, Jakoncic J, Desbonnet C, Garcia-Solache M, Rice LB, Page R, Peti W. (2018). The structures of penicillin-binding protein 4 (PBP4) and PBP5 from Enterococci provide structural insights into ?-lactam resistance. J Biol Chem. 293:18574-18584.

O’Daniel PI, Peng Z, Hualiang Pi, Sebastian A, Derong D, Edward S, Erika L, Marc A,, Takao Y, Valerie A, et al., (2014). Discovery of a New Class of Non-?-lactam Inhibitors of Penicillin-Binding Proteins with Gram-Positive Antibacterial Activity. Journal of the American Chemical Society 2014 136 (9), 3664-3672

Oladeji, O.S., Adelowo, F.E., Ayodele, D.T., Odelade, K.A. (2019). Phytochemistry and pharmacological activities of Cymbopogon citratus: A review.

Scientific African, 6: e00137

Sauvage E, Derouaux A, Fraipont C, Joris M, Herman R, Rocaboy M, Schloesser M, Dumas J, Kerff F, Nguyen-Distèche M, Charlier P. (2014). Crystal structure of penicillin-binding protein 3 (PBP3) from Escherichia coli. PLoS One. 9(5): e98042.

Sharma AD, Inderjeet Kaur. (2021). By-product ‘water’ of Eucalyptus globulus essential oil distillation as source of botanical insecticides: wealth from waste. Notulae Scientia Biologicae, 13, Article ID 10854.

Silva J., Abebeb W., Sousa S.M., Duarte V.G (2003). Analgesic and anti-inflammatory effects of essential oils of Eucalyptus. Journal of Ethnopharmacol., 89, 277–283

Simoes NG, Bettencourt AF, Monge N, Ribeiro IAC. (2017). Novel Antibacterial Agents: An Emergent Need to Win the Battle Against Infections. Mini Rev. Med. Chem. 17: 1364–1376

Siramon P., Ohtani Y. (2007). Antioxidative and antiradical activities of Eucalyptus camaldulensis leaf oils from Thailand. The Journal of Wood Science, 53: 498–504

Soviati N., Widyarman A.S. T (2020) he Effect Ant-Nest Plant (Myrmecodia pendans) Extract on Streptococcus sanguinis and Treponema denticola Biofilms. J. Indones. Dent. Assoc. 2020;3:11

Srimai V, Ramesh M, Parameshwar KS, Parthasarathy T. (2013). Computer-aided design of selective Cytochrome P450 inhibitors and docking studies of alkyl resorcinol derivatives. Med. Chem. Res., 22: 5314-5323

Straume D, Piechowiak KW, Olsen S, Stamsås GA, Berg KH, Kjos M, Heggenhougen MV, Alcorlo M, Hermoso JA, Håvarstein LS. (2020). Class A PBPs have a distinct and unique role in the construction of the pneumococcal cell wall. Proc Natl Acad Sci U S A. 17:6129-6138

Su Y.C., Ho C.L., Wang E.I., Chang S.T. (2006). Antifungal activities and chemical compositions of essential oils from leaves of four Eucalyptus. Taiwan J For Sci. 21, 49–61.

Welsh MA, Taguchi A, Schaefer K, Van Tyne D, Lebreton F, Gilmore MS, Kahne D, Walker S. (2017). Identification of a Functionally Unique Family of Penicillin-Binding Proteins. J Am Chem Soc. 13:17727-17730




DOI: https://doi.org/10.14421/biomedich.2023.121.225-232

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Copyright (c) 2023 Arun Dev Sharma, Inderjeet Kaur



Biology, Medicine, & Natural Product Chemistry
ISSN 2089-6514 (paper) - ISSN 2540-9328 (online)
Published by Sunan Kalijaga State Islamic University & Society for Indonesian Biodiversity.

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