, Volume 23, Issue 1, pp 27–40 | Cite as

Molecular docking studies of bioactive compounds from Annona muricata Linn as potential inhibitors for Bcl-2, Bcl-w and Mcl-1 antiapoptotic proteins

  • Mohamad Norisham Mohamad Rosdi
  • Shahkila Mohd Arif
  • Mohamad Hafizi Abu Bakar
  • Siti Aisyah Razali
  • Razauden Mohamed Zulkifli
  • Harisun Ya’akob
Original Paper


Annona muricata Linn or usually identified as soursop is a potential anticancer plant that has been widely reported to contain valuable chemopreventive agents known as annonaceous acetogenins. The antiproliferative and anticancer activities of this tropical and subtropical plant have been demonstrated in cell culture and animal studies. A. muricata L. exerts inhibition against numerous types of cancer cells, involving multiple mechanism of actions such as apoptosis, a programmed cell death that are mainly regulated by Bcl-2 family of proteins. Nonetheless, the binding mode and the molecular interactions of the plant’s bioactive constituents have not yet been unveiled for most of these mechanisms. In the current study, we aim to elucidate the binding interaction of ten bioactive phytochemicals of A. muricata L. to three Bcl-2 family of antiapoptotic proteins viz. Bcl-2, Bcl-w and Mcl-1 using an in silico molecular docking analysis software, Autodock 4.2. The stability of the complex with highest affinity was evaluated using MD simulation. We compared the docking analysis of these substances with pre-clinical Bcl-2 inhibitor namely obatoclax. The study identified the potential chemopreventive agent among the bioactive compounds. We also characterized the important interacting residues of protein targets which involve in the binding interaction. Results displayed that anonaine, a benzylisoquinoline alkaloid, showed a high affinity towards the Bcl-2, thus indicating that this compound is a potent inhibitor of the Bcl-2 antiapoptotic family of proteins.


Apoptosis Bcl-2 inhibitor Antiapoptotic proteins Annona muricata Linn Molecular docking MD simulation 



We deeply thank Dr Muhammad Helmi Nadri from Innovation Centre in Agritechnology for Advanced Bioprocessing, Universiti Teknologi Malaysia (UTM-ICA) for valuable comments and suggestions. This work was financially supported by Universiti Teknologi Malaysia and Ministry of Higher Education through Higher Institution Centres of Excellence (HICoE) research Grant (R.J130000.7846.4J261). MNMR was financially supported through Zamalah Scholarship, Universiti Teknologi Malaysia.


  1. 1.
    Ferlay J, Soerjomataram I, Ervik M et al. (2013) GLOBOCAN 2012 v1.0, Cancer Incidence and Mortality Worldwide: IARC CancerBase no. 11 [Internet], Lyon, France Accessed 28 Dec 2015
  2. 2.
    Siegel R, Naishadham D, Jemal A (2012) Cancer statistics, 2012. CA Cancer J Clin 62:10–29. CrossRefPubMedGoogle Scholar
  3. 3.
    Bray F, Jemal A, Grey N et al (2012) Global cancer transitions according to the Human Development Index (2008–2030): a population-based study. Lancet Oncol 13:790–801. CrossRefPubMedGoogle Scholar
  4. 4.
    Jemal A, Bray F, Center MM et al (2011) Global cancer statistics. CA Cancer J Clin 61:69–90. CrossRefPubMedGoogle Scholar
  5. 5.
    WHO (2012) Globocan 2012—home. Accessed 20 Dec 2016
  6. 6.
    IARC (2016) Globocan 2012. http://www.depiarcfr/Globocan:2012-2013. Accessed 4 Jan 2017
  7. 7.
    Hanahan D, Weinberg RA (2011) Hallmarks of cancer: the next generation. Cell 144:646–674CrossRefPubMedGoogle Scholar
  8. 8.
    Hanahan D, Weinberg RA (2000) The hallmarks of cancer. Cell 100:57–70CrossRefPubMedGoogle Scholar
  9. 9.
    Eimon PM, Ashkenazi A (2010) The zebrafish as a model organism for the study of apoptosis. Apoptosis 15:331–349. CrossRefPubMedGoogle Scholar
  10. 10.
    Dewson G, Kluck RM (2010) Bcl-2 family-regulated apoptosis in health and disease. Cell Health Cytoskelet 2:9–22. Google Scholar
  11. 11.
    Cory S, Huang DCS, Adams JM (2003) The Bcl-2 family: roles in cell survival and oncogenesis. Oncogene 22:8590–8607. CrossRefPubMedGoogle Scholar
  12. 12.
    Sharpe JC, Arnoult D, Youle RJ (2004) Control of mitochondrial permeability by Bcl-2 family members. Biochim Biophys Acta 1644:107–113. CrossRefPubMedGoogle Scholar
  13. 13.
    Adams JM, Cory S (2007) The Bcl-2 apoptotic switch in cancer development and therapy. Oncogene 26:1324–1337. CrossRefPubMedPubMedCentralGoogle Scholar
  14. 14.
    Kim H, Rafiuddin-Shah M, Tu H-C et al (2006) Hierarchical regulation of mitochondrion-dependent apoptosis by BCL-2 subfamilies. Nat Cell Biol 8:1348–1358. CrossRefPubMedGoogle Scholar
  15. 15.
    García-Sáez AJ (2012) The secrets of the Bcl-2 family. Cell Death Differ 19:1733–1740. CrossRefPubMedPubMedCentralGoogle Scholar
  16. 16.
    Wei MC, Zong WX, Cheng EH et al (2001) Proapoptotic BAX and BAK: a requisite gateway to mitochondrial dysfunction and death. Science 292:727–730. CrossRefPubMedPubMedCentralGoogle Scholar
  17. 17.
    Letai A, Bassik MC, Walensky LD et al (2002) Distinct BH3 domains either sensitize or activate mitochondrial apoptosis, serving as prototype cancer therapeutics. Cancer Cell 2:183–192. CrossRefPubMedGoogle Scholar
  18. 18.
    Kuwana T, Bouchier-Hayes L, Chipuk JE et al (2005) BH3 domains of BH3-only proteins differentially regulate Bax-mediated mitochondrial membrane permeabilization both directly and indirectly. Mol Cell 17:525–535. CrossRefPubMedGoogle Scholar
  19. 19.
    Certo M, Moore VDG, Nishino M et al (2006) Mitochondria primed by death signals determine cellular addiction to antiapoptotic BCL-2 family members. Cancer Cell 9:351–365. CrossRefPubMedGoogle Scholar
  20. 20.
    Llambi F, Moldoveanu T, Tait SWG et al (2011) A unified model of mammalian BCL-2 protein family interactions at the mitochondria. Mol Cell 44:517–531. CrossRefPubMedPubMedCentralGoogle Scholar
  21. 21.
    Kirkin V, Joos S, Zörnig M (2004) The role of Bcl-2 family members in tumorigenesis. Biochim Biophys Acta Mol Cell Res 1644:229–249. CrossRefGoogle Scholar
  22. 22.
    Wendt MD (2008) Discovery of ABT-263, a Bcl-family protein inhibitor: observations on targeting a large protein-protein interaction. Expert Opin Drug Discov 3:1123–1143. CrossRefPubMedGoogle Scholar
  23. 23.
    Bajwa N, Liao C, Nikolovska-Coleska Z (2012) Inhibitors of the anti-apoptotic Bcl-2 proteins: a patent review. Expert Opin Ther Pat 22:37–55. CrossRefPubMedGoogle Scholar
  24. 24.
    Baell JB, Huang DCS (2002) Prospects for targeting the Bcl-2 family of proteins to develop novel cytotoxic drugs. Biochem Pharmacol 64:851–863. CrossRefPubMedGoogle Scholar
  25. 25.
    Enyedy IJ, Huang Y, Long YQ et al (2001) Discovery of small-molecule inhibitors of Bcl-2 through structure-based computer screening. J Med Chem 44:4313–4324. CrossRefPubMedGoogle Scholar
  26. 26.
    Wang J-L, Liu D, Zhang Z-J et al (2000) Structure-based discovery of an organic compound that binds Bcl-2 protein and induces apoptosis of tumor cells. Proc Natl Acad Sci USA 97:7124–7129CrossRefPubMedPubMedCentralGoogle Scholar
  27. 27.
    Harazono Y, Nakajima K, Raz A (2014) Why anti-Bcl-2 clinical trials fail: a solution. Cancer Metastasis Rev 33:285–294. CrossRefPubMedPubMedCentralGoogle Scholar
  28. 28.
    Ezirim AU, Okochi VI, James AB, Adebeshi OA, Ogunnowo O (2013) Induction of apoptosis in myelogenous leukemic K562 cells by ethanolic leaf extract of Annona muricata L. Glob J Res Med Plants Indig Med 2:142–151Google Scholar
  29. 29.
    Moghadamtousi SZ, Kadir HA, Paydar M et al (2014) Annona muricata leaves induced apoptosis in A549 cells through mitochondrial-mediated pathway and involvement of NF-kappa B. BMC Complement Altern Med 14:299. CrossRefPubMedPubMedCentralGoogle Scholar
  30. 30.
    Dayeef AYM, Karyono S, Sujuti H (2013) The influence of Annona muricata leaves extract in damaging kidney cell and inducing caspase-9 activity. J Pharm Biol Sci 8:48–52Google Scholar
  31. 31.
    Pieme CA, Kumar SG, Dongmo MS et al (2014) Antiproliferative activity and induction of apoptosis by Annona muricata (Annonaceae) extract on human cancer cells. BMC Complement Altern Med 14:516. CrossRefPubMedPubMedCentralGoogle Scholar
  32. 32.
    Dai Y, Hogan S, Schmelz EM et al (2011) Selective growth inhibition of human breast cancer cells by graviola fruit extract in vitro and in vivo involving downregulation of EGFR expression. Nutr Cancer 63:795–801. CrossRefPubMedGoogle Scholar
  33. 33.
    De Pedro N, Cautain B, Melguizo A et al (2013) Mitochondrial complex i inhibitors, acetogenins, induce HepG2 cell death through the induction of the complete apoptotic mitochondrial pathway. J Bioenerg Biomembr 45:153–164. CrossRefPubMedGoogle Scholar
  34. 34.
    Morris GM, Ruth H, Lindstrom W et al (2009) Software news and updates AutoDock4 and AutoDockTools4: automated docking with selective receptor flexibility. J Comput Chem 30:2785–2791. CrossRefPubMedPubMedCentralGoogle Scholar
  35. 35.
    Rizvi SMD, Shakil S, Haneef M (2013) A simple click by click protocol to perform docking: Autodock 4.2 made easy for non-bioinformaticians. EXCLI J 12:830–857Google Scholar
  36. 36.
    Kelly LA, Mezulis S, Yates C et al (2015) The Phyre2 web portal for protein modelling, prediction, and analysis. Nat Protoc 10:845–858. CrossRefGoogle Scholar
  37. 37.
    Colovos C, Yeates TO (1993) Verification of protein structures: patterns of nonbonded atomic interactions. Protein Sci 2:1511–1519. CrossRefPubMedPubMedCentralGoogle Scholar
  38. 38.
    Bowie J, Luthy R, Eisenberg D (1991) A method to identify protein sequences that fold into a known three-dimensional structure. Science 253:164–170. CrossRefPubMedGoogle Scholar
  39. 39.
    Lüthy R, Bowie JU, Eisenberg D (1992) Assessment of protein models with three-dimensional profiles. Nature 356:83–85. CrossRefPubMedGoogle Scholar
  40. 40.
    Lovell SC, Davis IW, Arendall WB et al (2003) Structure validation by Calpha geometry: phi,psi and Cbeta deviation. Proteins 50:437–450. CrossRefPubMedGoogle Scholar
  41. 41.
    Pettersen EF, Goddard TD, Huang CC et al (2004) UCSF chimera—a visualization system for exploratory research and analysis. J Comput Chem 25:1605–1612. CrossRefPubMedGoogle Scholar
  42. 42.
    Abraham MJ, Murtola T, Schulz R et al (2015) Gromacs: high performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX 1–2:19–25. CrossRefGoogle Scholar
  43. 43.
    Schmid N, Eichenberger AP, Choutko A et al (2011) Definition and testing of the GROMOS force-field versions 54A7 and 54B7. Eur Biophys J 40:843–856. CrossRefPubMedGoogle Scholar
  44. 44.
    Schüttelkopf AW, Van Aalten DMF (2004) PRODRG: a tool for high-throughput crystallography of protein-ligand complexes. Acta Crystallogr Sect D Biol Crystallogr 60:1355–1363. CrossRefGoogle Scholar
  45. 45.
    Essmann U, Perera L, Berkowitz ML et al (1995) A smooth particle mesh Ewald method. J Chem Phys 103:8577–8593. CrossRefGoogle Scholar
  46. 46.
    Hess B, Bekker H, Berendsen HJC, Fraaije JGEM (1997) LINCS: a linear constraint solver for molecular simulations. J Comput Chem 18:1463–1472CrossRefGoogle Scholar
  47. 47.
    Shimizu S, Eguchi Y, Kamiike W et al (1996) Induction of apoptosis as well as necrosis by hypoxia and predominant prevention of apoptosis by Bcl-2 and Bcl-XL. Cancer Res 56:2161–2166PubMedGoogle Scholar
  48. 48.
    Hockenbery DM, Oltvai ZN, Yin XM et al (1993) Bcl-2 functions in an antioxidant pathway to prevent apoptosis. Cell 75:241–251. CrossRefPubMedGoogle Scholar
  49. 49.
    Nakashima T, Miura M, Hara M (2000) Tetrocarcin A inhibits mitochondrial functions of Bcl-2 and suppresses its anti-apoptotic activity. Cancer Res 60:1229–1235PubMedGoogle Scholar
  50. 50.
    Huang Z (2000) Bcl-2 family proteins as targets for anticancer drug design. Oncogene 19:6627–6631. CrossRefPubMedGoogle Scholar
  51. 51.
    Antony P, Vijayan R (2016) Acetogenins from Annona muricata as potential inhibitors of antiapoptotic proteins: a molecular modeling study. Drug Des Devel Ther 10:1399–1410. PubMedPubMedCentralGoogle Scholar
  52. 52.
    Petros A, Olejniczak E, Fesik S (2004) Structural biology of the Bcl-2 family of proteins. Biochim Biophys Acta 1644(2):83–94CrossRefPubMedGoogle Scholar
  53. 53.
    Souers AJ, Leverson JD, Boghaert ER et al (2013) ABT-199, a potent and selective BCL-2 inhibitor, achieves antitumor activity while sparing platelets. Nat Med 19:202–208. CrossRefPubMedGoogle Scholar
  54. 54.
    Chen CY, Liu TZ, Tseng WC et al (2008) (-)-Anonaine induces apoptosis through Bax- and caspase-dependent pathways in human cervical cancer (HeLa) cells. Food Chem Toxicol 46:2694–2702. CrossRefPubMedGoogle Scholar
  55. 55.
    Chen B-H, Chang H-W, Huang H-M et al (2011) (-)-Anonaine induces DNA damage and inhibits growth and migration of human lung carcinoma h1299 cells. J Agric Food Chem 59:2284–2290. CrossRefPubMedGoogle Scholar
  56. 56.
    Mohamed SM, Hassan EM, Ibrahim N (2010) Cytotoxic and antiviral activities of aporphine alkaloids of Magnolia grandiflora L. Nat Prod Res 24:1395–1402. CrossRefPubMedGoogle Scholar
  57. 57.
    Meng X-Y, Zhang H-X, Mezei M, Cui M (2011) Molecular docking: a powerful approach for structure-based drug discovery. Curr Comput Aided Drug Des 7:146–157. CrossRefPubMedPubMedCentralGoogle Scholar
  58. 58.
    Plewczynski D, Łaźniewski M, Augustyniak R, Ginalski K (2011) Can we trust docking results? Evaluation of seven commonly used programs on PDBbind database. J Comput Chem 32:742–755. CrossRefPubMedGoogle Scholar
  59. 59.
    Chaitanya M, Babajan B, Anuradha CM et al (2010) Exploring the molecular basis for selective binding of Mycobacterium tuberculosis Asp kinase toward its natural substrates and feedback inhibitors: a docking and molecular dynamics study. J Mol Model 16:1357–1367. CrossRefPubMedGoogle Scholar
  60. 60.
    Shamriz S, Ofoghi H (2016) Design, structure prediction and molecular dynamics simulation of a fusion construct containing malaria pre-erythrocytic vaccine candidate, PfCelTOS, and human interleukin 2 as adjuvant. BMC Bioinformatics 17:71. CrossRefPubMedPubMedCentralGoogle Scholar
  61. 61.
    Esmaili E, Shahlaei M (2015) Analysis of the flexibility and stability of the structure of magainin in a bilayer, and in aqueous and nonaqueous solutions using molecular dynamics simulations. J Mol Model 21:1–15. CrossRefGoogle Scholar
  62. 62.
    Lobanov MI, Bogatyreva NS, Galzitskaia OV (2008) Radius of gyration is indicator of compactness of protein structure. Mol Biol (Mosk) 42:701–706. CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2017

Authors and Affiliations

  • Mohamad Norisham Mohamad Rosdi
    • 1
  • Shahkila Mohd Arif
    • 2
  • Mohamad Hafizi Abu Bakar
    • 3
  • Siti Aisyah Razali
    • 4
  • Razauden Mohamed Zulkifli
    • 5
  • Harisun Ya’akob
    • 1
    • 6
  1. 1.Department of Bioprocess and Polymer Engineering, Faculty of Chemical and Energy EngineeringUniversiti Teknologi MalaysiaSkudaiMalaysia
  2. 2.Department of Biotechnology and Medical Engineering, Faculty of Biosciences and Medical EngineeringUniversiti Teknologi MalaysiaSkudaiMalaysia
  3. 3.Bioprocess Technology Division, School of Industrial TechnologyUniversiti Sains MalaysiaGelugorMalaysia
  4. 4.Bioinformatics Research Group, Faculty of Biosciences and Medical EngineeringUniversiti Teknologi MalaysiaSkudaiMalaysia
  5. 5.Department of Bioscience and Health Sciences, Faculty of Biosciences and Medical EngineeringUniversiti Teknologi MalaysiaSkudaiMalaysia
  6. 6.Institute of Bioproduct DevelopmentUniversiti Teknologi MalaysiaSkudaiMalaysia

Personalised recommendations