Molecular Docking, Dynamics Simulation, and Scanning Electron Microscopy (SEM) Examination of Clinically Isolated Mycobacterium tuberculosis by Ursolic Acid: A Pentacyclic Triterpenes

Dian Ayu Eka Pitaloka(1*), Sophi Damayanti(2), Aluicia Anita Artarini(3), Elin Yulinah Sukandar(4)

(1) Department Pharmacology-Clinical Pharmacy, School of Pharmacy, Institut Teknologi Bandung, Jl. Ganesa no. 10, Bandung 40132, West Java, Indonesia
(2) Department of Pharmacochemistry, School of Pharmacy, Institut Teknologi Bandung, Jl. Ganesa no. 10, Bandung 40132, West Java, Indonesia
(3) Department of Pharmaceutical Biotechnology, School of Pharmacy, Institut Teknologi Bandung,Jl. Ganesa no. 10, Bandung 40132, West Java, Indonesia
(4) Department of Pharmacology and Clinical Pharmacy, School of Pharmacy, Jl. Ganesa no. 10, Bandung 40132, West Java, Indonesia
(*) Corresponding Author


The purpose of this study was to analyze the inhibitory action of ursolic acid (UA) as an antitubercular agent by computational docking studies and molecular dynamics simulations. The effect of UA on the cell wall of Mycobacterium tuberculosis (MTB) was evaluated by using Scanning Electron Microscopy (SEM). UA was used as a ligand for molecular interaction and investigate its binding activities to a group of proteins involved in the growth of MTB and the biosynthesis of the cell wall. Computational docking analysis was performed by using autodock 4.2.6 based on scoring functions. UA binding was confirmed by 30 ns molecular dynamics simulation using gromacs 5.1.1. H37Rv sensitive strain and isoniazid-resistant strain were used in the SEM study. UA showed to have the optimum binding affinity to inhA (Two-trans-enoyl-ACP reductase enzyme involved in elongation of fatty acid) with the binding energy of -9.2 kcal/mol. The dynamic simulation showed that the UA-inhA complex relatively stable and found to establish hydrogen bond with Thr196 and Ile194. SEM analysis confirms that UA treatment in both sensitive strain and resistant strain affected the morphology cell wall of MTB. This result indicated that UA could be one of the potential ligands for the development of new antituberculosis drugs.


antituberculosis; ursolic acid; docking molecular; molecular dynamics simulation; Scanning Electron Microscopy (SEM)

Full Text:

Full Text PDF


[1] Ducati, R.G., Ruffino-Netto, A., Basso, L.A., and Santos, D.S., 2006, The resumption of consumption – a review on tuberculosis, Mem. Inst. Oswaldo Cruz, 101 (1), 697–714.

[2] Jassal, M.S., and Bishai, W.R., 2015, The epidemiology and challenges to the elimination of global tuberculosis, Clin. Infect. Dis., 50 (Suppl. 3), 156–164.

[3] World Health Organization, Tuberculosis,, accessed on 31 January 2018.

[4] Kim, K.A., Lee, J.S., Park, H.J., Kim, C.J., Shim, I.S., Kim, N.J., Han, S.M., and Lim, S., 2004, Inhibition of cytochrome P450 activities by oleanolic acid and ursolic acid in human liver microsomes, Life Sci., 74 (22), 2769–2779.

[5] Ku, C.M., and Lin, J.Y., 2013, Anti-inflammatory effects of 27 selected terpenoid compounds tested through modulating Th1/Th2 cytokine secretion profiles using murine primary splenocytes, Food Chem., 141 (2), 1104–1113.

[6] Shanmugam, M.K., Dai, X., Kumar, A.P., Tan, B.K.H., Sethi, G., and Bishayee, A., 2013, Ursolic acid in cancer prevention and treatment: Molecular targets, pharmacokinetics and clinical studies, Biochem. Pharmacol., 85 (11), 1579–1587.

[7] Liobikas, J., Majiene, D., Trumbeckaite, S, Kursvietiene, L., Masteikova, R., Kopustinskiene, D.M., Savickas, A., and Bernatoniene, J., 2011, Uncoupling and antioxidant effects of ursolic acid in isolated rat heart mitochondria, J. Nat. Prod., 74 (7), 1640–1644.

[8] Ali, M.S., Ibrahim, S.A., Jalil, S., and Choudhary, M.I., 2007, Ursolic acid: A potent inhibitor of superoxides produced in the cellular system, Phytother. Res., 21 (6), 558–561.

[9] D’Abrosca, B., Fiorentino, A., Monaco, P., and Pacifico, S., 2005, Radical-scavenging activities of new hydroxylated ursane triterpenes from cv. Annurca apples, Chem. Biodivers., 2 (7), 953–958.

[10] Mallavadhani, U.V., Mahapatra, A., Jamil, K., and Reddy, P.S., 2004, Antimicrobial activity of some pentacyclic triterpenes and their synthesized 3-O-lipophilic chains, Biol. Pharm. Bull., 27 (10), 1576–1579.

[11] Silva, M.L., David, J.P., Silva, L.C.R.C., Santos, R.A.F., David, J.M., Lima, L.S., Reis, P.S., and Fontana, R., 2012, Bioactive oleanane, lupane and ursane triterpene acid derivatives, Molecules, 17 (10), 12197–12205.

[12] Kurek, A., Nadkowska, P., Pliszka, S., and Wolska, K.I., 2012, Modulation of antibiotic resistance in bacterial pathogens by oleanolic acid and ursolic acid, Phytomedicine, 19 (6), 515–519.

[13] Pitaloka, D.A.E., and Sukandar, E.Y., 2017, In vitro study of ursolic acid combination first-line antituberculosis drugs against drug-sensitive and drug-resistant strains of Mycobacterium tuberculosis, Asian J. Pharm. Clin. Res., 10 (4), 216–218.

[14] Martins, D., Carrion, L.L., Ramos, D.F., Salomé, K.S., da Silva, P.E.A., Andersson, B., Cleverson Agner Ramos, C.A., and Cecilia Veronica Nunez, C.V., 2014, Anti-tuberculosis activity of oleanolic and ursolic acid isolated from the dichloromethane extract of leaves from Duroia macrophylla, BMC Proc., 8 (Suppl. 4), P3.

[15] Marrakchi, H., Lanéelle, G., and Quémard, A., 2010, InhA, a target of the antituberculous drug isoniazid is involved in a mycobacterial fatty acid elongation system, FAS-II, Microbiology, 146 (2), 289–296.

[16] Ducasse-Cabanot, S., Cohen-Gonsaud, M., Marrakchi, H., Nguyen, M., Zerbib, D., Bernadou, J., Daffé, M., Labesse, G., and Quémard, A., 2004, In vitro inhibition of the Mycobacterium tuberculosis β-ketoacyl-acyl carrier protein reductase MabA by isoniazid, Antimicrob. Agents Chemother., 48 (1), 242–249.

[17] Takayama, K., Wang, C., and Besra, G.S., 2005, Pathway to synthesis and processing of mycolic acids in Mycobacterium tuberculosis, Clin. Microbiol. Rev., 18 (1), 81–101.

[18] Björkelid, C., Bergfors, T., Raichurkar, A.K., Mukherjee, K., Malolanarasimhan, K., Bandodkar, B., and Jones, T.A., 2013, Structural and biochemical characterization of compounds inhibiting Mycobacterium tuberculosis pantothenate kinase, J. Biol. Chem., 208 (25), 18260–18270.

[19] Ramaswamy, S., and Musser, J.M., 1998, Molecular genetic basis of antimicrobial agent resistance in Mycobacterium tuberculosis: 1998 update, Tuber. Lung Dis., 79 (1), 3–29.

[20] Campbell, E.A., Korzheva, N., Mustaev, A., Murakami, K., Nair, S., Goldfarb, A., and Darst, S.A., 2011, Structural mechanism for Rifampicin inhibition of bacterial RNA polymerase, Cell, 104 (6), 901–912.

[21] Gasteiger, J., and Marsili, M., 1980, Iterative partial equalization of orbital electronegativity-a rapid access to atomic charges, Tetrahedron, 36 (22), 3219–3228.

[22] Goodsell, D.S., Morris, G.M., and Olson, A.J., 1996, Automated docking of flexible ligands: applications of autodock, J. Mol. Recognit., 9(1), 1–5.

[23] Morris, G.M., Goodsell, D.S., Halliday, R.S., Huey, R., Hart, W.E., Belew, R.K., and Olson, A.J., 1998, Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function, J. Comput. Chem., 19 (14), 1639–1662.

[24] Caims, D., Michalitsi, E., Jenkins, T.C., and Mackay, S.P., 2002, Molecular modelling and cytotoxicity of substituted anthraquinones as inhibitors of human telomerase, Bioorg. Med. Chem., 10 (3), 803–807.

[25] Humphrey, W., Dalke, A., and Schulten, K., 1996, VMD: Visual molecular dynamics, J. Mol. Graphics, 14 (1), 33–38.

[26] De Logu, A., Onnis, V., Saddi, B., Congiu, C., Schivo, M.L., and Cocco, M.T., 2002, Activity of a new class of isonicotinoylhydrazones used alone and in combination with isoniazid, rifampicin, ethambutol, para-aminosalicylic acid and clofazimine against Mycobacterium tuberculosis, J. Antimicrob. Chemother., 49 (2), 275–282.

[27] Jyoti, M.A., Zerin, T., Kim, T.H., Hwang, T.S., Jang, W.S., Nam, K.W., and Song, H.Y., 2015, In vitro effect of ursolic acid on the inhibition of Mycobacterium tuberculosis and its cell wall mycolic acid, Pulm. Pharmacol. Ther., 33, 17–24.

[28] Zhang Y., and Yew, W.W., 2015, Mechanism of drug resistance in Mycobacterium tuberculosis: Update 2015, Int. J. Tuberc. Lung Dis., 19 (11), 1276–1289

[29] Shoichet, B.K., McGovern, S.L., Wei, B., and Irwin, J.J., 2002, Lead discovery using molecular docking, Curr. Opin. Chem. Biol., 6 (4), 436–446.

[30] Rozwarski, D.A., Vilchèze, C., Sugantino, M., Bittman, R., and Sacchettini, J.C., 1999, Crystal structure of the Mycobacterium tuberculosis enoyl-ACP reductase, InhA, in complex with NAD+ and a C16 fatty acyl substrate, J. Biol. Chem., 274 (22), 15582–15589.

[31] Rosado, L.A., Caceres, R.A., de Azevedo Jr, W.F., Basso, L.A., and Santos, D.S., 2012, Role of serine140 in the mode of action of Mycobacterium tuberculosis β-ketoacyl-ACP reductase (MabA), BMC Res. Note, 5, 526.

[32] Cheek, S., Zhang, H., and Grishin, N.V., 2002, Sequence and structure classification of kinases, J. Mol. Biol., 320 (4), 855–881.

[33] Chetnani, B., Kumar, P., Surolia, A., and Vijayan, M., 2010, M. tuberculosis pantothenate kinase: Dual substrate specificity and unusual changes in ligand locations, J. Mol. Biol., 400 (2), 171–185.

[34] Sankaranarayanan, R., Saxena, P., Marathe, U.B., Gokhale, R.S., Shanmugam, V.M., and Rukmini, R., 2004, A novel tunnel in mycobacterial type III polypeptide synthase reveals the structural basis for generating diverse metabolites, Nat. Struct. Mol. Biol., 11 (9), 894–900.

[35] Andrade, B., Souza, C., and Goes-Neto, A., 2013, Molecular docking between the RNA polymerase of the Moniliophthora perniciosa mitochondrial plasmid and rifampicin produces a highly stable complex, Theor. Biol. Med. Model, 10(15), 10–15.


Article Metrics

Abstract views : 4827 | views : 4154

Copyright (c) 2018 Indonesian Journal of Chemistry

Creative Commons License
This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.


Indonesian Journal of Chemistry (ISSN 1411-9420 /e-ISSN 2460-1578) - Chemistry Department, Universitas Gadjah Mada, Indonesia.

Analytics View The Statistics of Indones. J. Chem.