Isolation and Antibacterial Activity by in vitro and in silico Approach of 6-Deoxyjacareubin Compound from Garcinia latissima Miq. Fruit

Neneng Siti Silfi Ambarwati(1), Berna Elya(2), Amarila Malik(3), Yuditya Artha(4), Islamudin Ahmad(5), Azminah Azminah(6), Muhammad Hanafi(7*), Hanita Omar(8)

(1) Faculty of Engineering, Universitas Negeri Jakarta, Jl. Rawamangun Muka, East Jakarta 13220, Indonesia
(2) Faculty of Pharmacy, Universitas Indonesia, UI Depok Campus, Depok 16424, West Java, Indonesia
(3) Faculty of Pharmacy, Universitas Indonesia, UI Depok Campus, Depok 16424, West Java, Indonesia
(4) Faculty of Pharmacy, Universitas Indonesia, UI Depok Campus, Depok 16424, West Java, Indonesia
(5) Department of Pharmaceutical Sciences, Faculty of Pharmacy, Mulawarman University, Jl. Kuaro, Gn. Kelua, Samarinda 75119, East Kalimantan, Indonesia
(6) Faculty of Pharmacy, Universitas Surabaya, Jl. Raya Kalirungkut, Surabaya 60293, East Java, Indonesia
(7) Research Centre for Chemistry–Indonesian Institute of Sciences, Kawasan PUSPIPTEK Serpong, Tangerang Selatan 15314, Banten, Indonesia
(8) Chemistry Division, Centre for Foundation Studies in Science, University of Malaya, Kuala Lumpur, Malaysia
(*) Corresponding Author


The previous research showed that the fraction C from active extract of Garcinia latissima Miq. fruit was active against Bacillus subtilis. This study aims to isolate and identify the active compound as an antibacterial agent from the fraction C. Fraction C was purified by recrystallization using chloroform and n-hexane solvents and then isolated using preparative-thin layer chromatography-silica gel 60 GF254 to give a yellow compound. The antibacterial activity was determined using microdilution with thiazolyl blue tetrazolium bromide indicator against B. subtilis American Type Culture Collection 6633. The isolate was identified using UV-Vis, IR, MS, Proton Nuclear Magnetic Resonance (1H-NMR) and carbon NMR (13C-NMR), and NMR-2D techniques including HMQC and HMBC. Based on the spectroscopic analysis and literature review, the compound was identified as 6-deoxyjacareubin, which is a new compound from Garcinia latissima Miq. The 6-deoxyjacareubin showed antibacterial activity with MIC value of 156.25 ppm and was categorized as a weak antibacterial agent because the MIC value was more than 100 ppm. According to in silico approach to the docking study, 6-deoxyjacareubin showed similar hydrophobic interaction with several amino acid residues including C2565, C2589, G2484, U2590, and U5588 between a native ligand.


6-deoxyjacareubin; antibacterial; Bacillus subtilis; Garcinia latissima Miq.

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[1] Kochuthressia, K.P., Britto, S.J., Jaseentha, M.O., and Raphael, R., 2012, In vitro antimicrobial evaluation of Kaempferia galanga L. rhizome extract, Am. J. Biotechnol. Mol. Sci., 2 (1), 1–5.

[2] Sholikhah, E.N., 2016, Indonesian medicinal plants as sources of secondary metabolites for pharmaceutical industry, J. Med. Sci., 48 (4), 226–239.

[3] Nascimento, G.G.F., Locatelli, J., Freitas, P.C., and Silva, G.L., 2000, Antibacterial activity of plant extracts and phytochemicals on antibiotic-resistant bacteria, Braz. J. Microbiol., 31 (4), 247–256.

[4] Dzotam, J.K., and Kuete, V., 2017, Antibacterial and antibiotic-modifying activity of methanol extracts from six Cameroonian food plants against multidrug-resistant enteric bacteria, BioMed Res. Int., 2017, 1583510.

[5] Valgas, C., de Souza, S.M., Smânia, E.F.A., and Smania, Jr.A., 2007, Screening methods to determine antibacterial activity of natural products, Braz. J. Microbiol., 38 (2), 369–380.

[6] Ambarwati, N.S.S., Elya, B., Malik, A., and Hanafi, M., 2017, Phytochemical and antimicrobial studies on Garcinia latissima Miq. fruits extract, Asian J. Pharm. Clin. Res., 10 (7), 230–232.

[7] Ambarwati, N.S.S., Malik, A., Listari, A.T., Nirwana, Elya, B., and Hanafi, M., 2017, Antibacterial activity of fractions of ethyl acetate extract of Garcinia latissima Miq. fruits, Asian J. Pharm. Clin. Res., 10 (17), 81–84.

[8] Bhakiaraj, D., Elavarasan, T., and Gopalakrishnan, M., 2014, Synthesis, spectral analysis, antimicrobial evaluation and molecular docking studies of some novel 3,5-dichloro-2,6-diarylpiperidin-4-ones, Der Pharma Chem., 6 (5), 243–250.

[9] Lin, J.T., Connelly, M.B., Amolo, C., Otani, S., and Yaver, D.S., 2005, Global transcriptional response of Bacillus subtilis to treatment with subinhibitory concentrations of antibiotics that inhibit protein synthesis, Antimicrob. Agents Chemother., 49 (5), 1915–1926.

[10] Champney, W.S., and Burdine, R., 1995, Macrolide antibiotics inhibit 50S ribosomal subunit assembly in Bacillus subtilis and Staphylococcus aureus, Antimicrob. Agents Chemother., 39 (9), 2141–2144.

[11] Pechère, J.C., and Kaplan, E.L., 2004, Streptococcal Pharyngitis: Optimal Management, Karger Medical and Scientific Publishers, Basel, Switzerland.

[12] Harborne, J.B., Baxter, H., and Moss, G.P., 1999, Phytochemical Dictionary A Handbook of Bioactive Compounds from Plants, 2nd Ed., CRC Press, Boca Raton, Florida.

[13] Iinuma, M., Tosa, H., Tanaka, T., and Yonemori, S., 1994, Two new xanthones in the underground part of Calophyllum inophyllum, Heterocycles, 37 (2), 833–838.

[14] Oo, W.M., 2018, Pharmacological properties of Calophyllum inophyllum – Updated review, Int. J. Photochem. Photobiol., 2 (1), 28–32.

[15] Lim, T.K., 2012, Edible Medicinal and Non-Medicinal Plants, Springer, Netherlands.

[16] Schlünzen, F., Zarivach, R., Harms, J., Bashan, A., Tocilj, A., Albrecht, R., Yonath, A., and Franceschi, F., 2001, Structural basis for the interaction of antibiotics with the peptidyl transferase centre in eubacteria, Nature, 413 (6858), 814–821.

[17] Dewick, P.M., 2006, Essentials of Organic Chemistry for Students of Pharmacy, Medicinal Chemistry and Biological Chemistry, 1st Ed., Wiley, Hoboken, New Jersey.

[18] Wu, Y.P., Zhao, W., Xia, Z.Y., Kong, G.H., Lu, X.P., Hu, Q.F., and Gao, X.M., 2013, Three novel xanthones from Garcinia paucinervis and their anti-TMV activity, Molecules, 18 (8), 9663–9669.

[19] Yi, B., Hu, L., Mei, W., Zhou, K., Wang, H., Luo, Y., Wei, X., and Dai, H., 2010, Antioxidant phenolic compounds of cassava (Manihot esculenta) from Hainan, Molecules, 16 (12), 10157–10167.

[20] Hostettmann, K., Marston, A., and Hostettmann, M., 1998, Preparative Chromatography Techniques Applications in Natural Product Isolation, 2nd Ed., Springer-Verlag, Berlin Heidelberg.

[21] Kurniawati, P.T., Soetjipto, H., and Limantara, L., 2007, Antioxidant and antibacterial activities of bixin pigment from annatto (Bixa orellana L.) seeds, Indones. J. Chem., 7 (1), 88–92.

[22] Su, P.W., Yang, C.H., Yang, J.F., Su, P.Y., and Chuang, L.Y., 2015, Antibacterial activities and antibacterial mechanism of Polygonum cuspidatum extracts against nosocomial drug-resistant pathogens, Molecules, 20 (6), 11119–11130.

[23] Gupta, R., Beg, Q.K., and Lorenz, P., 2002, Bacterial alkaline proteases: Molecular approaches and industrial applications, Appl. Microbiol. Biotechnol., 59 (1), 15–32.

[24] Hostettmann, K., and Hostettmann, M., 1989, “Xanthones” in Methods in Plant Biochemistry, vol. 1, Eds. Harborne, J.B., Academic Press, London, 493–508.

[25] Narasimhan, S., Maheshwaran, S., Abu-Yousef, I.A., Majdalawieh, A.F., Rethavathi, J., Das, P.E., and Poltronieri, P., 2017, Anti-bacterial and anti-fungal activity of xanthones obtained via semi-synthetic modification of α-mangostin from Garcinia mangostana, Molecules, 22 (2), 275.

[26] Fukai, T., Oku, Y., Hou, A.J., Yonekawa, M., and Terada, S., 2004, Antimicrobial activity of hydrophobic xanthones from Cudrania cochinchinensis against Bacillus subtilis and methicillin‐resistant Staphylococcus aureus, Chem. Biodivers., 1 (9), 1385–1390.

[27] Awouafack, M.D., McGaw, L.J., Gottfried, S., Mbouangouere, R., Tane, P., Spiteller, M., and Eloff, J.N., 2013, Antimicrobial activity and cytotoxicity of the ethanol extract, fractions and eight compounds isolated from Eriosema robustum (Fabaceae), BMC Complem. Altern. Med., 13, 289.

[28] Liu, K., and Kokubo, H., 2017, Exploring the stability of ligand binding modes to proteins by molecular dynamics simulations: A cross-docking study, J. Chem. Inf. Model., 57 (10), 2514–2522.


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