Breast cancer is the second leading cause of cancer death in women only next to lung cancer. In normal cells, BRCA1 and BRCA2 (breast cancer susceptibility gene 1 and breast cancer susceptibility gene 2) ensure the stability of DNA and also prevent uncontrolled cell growth. Mutation of these genes is linked to the development of hereditary breast and ovarian cancers. Considering the lacunae of reliable and potential drugs to cure the life threatening breast cancer, the present study has focused on molecular computational analysis to identify the potential compounds, derived from mangrove ecosystem, which can block the mutated gene (BRCA1) responsible for the breast cancer. Six compounds were tested against the carcinogenic protein. The 3D crystal structure of the protein was retrieved from protein data bank (PDB) and the protein binding sites of the test compounds were identified. The results revealed that among six compounds, triterpenoid, stigmasterol and pyrethrin were found efficient in destroying the protein (BRCA1) responsible for breast cancer

Sunilkumar Sahu, Senthil Raja, P. Kathiresan, K.

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International Multidisciplinary Research Journal 2011, 1/1:09-12 www.irjs.info/  www.scholarjournals.org   IRMJ-Health Science Insilico docking analysis of mangrove-derived compounds against breast cancer protein (BRCA1) Senthil Raja*, P. Kathiresan, K. Sunilkumar Sahu Department of Zoology, Annamalai university, Annamalainagar,Chidambarm,India. CAS in Marine Biology, Faculty of Marine Sciences, Annamalai University, Parangipettai 608 502, India Abstract: Breast cancer is the second leading cause of cancer death in women only next to lung cancer. In normal cells, BRCA1 and BRCA2 (breast cancer susceptibility gene 1 and breast cancer susceptibility gene 2) ensure the stability of DNA and also prevent uncontrolled cell growth. Mutation of these genes is linked to the development of hereditary breast and ovarian cancers. Considering the lacunae of reliable and potential drugs to cure the life threatening breast cancer, the present study has focused on m o l e c u l a r  computational analysis to identify the potential compounds, derived from mangrove e c o s y s t e m , which can block the mutated gene (BRCA1) responsible for the breast cancer. Six compounds were tested against the carcinogenic protein. The 3D crystal structure of the protein was retrieved from protein data bank (PDB) and the protein binding sites of the test compounds were identified. The results revealed t h a t  a m o n g  s i x  c o m p o u n d s ,  t r i t e r p e n o i d ,  s t i g m a s t e r o l  a n d  pyrethrin w e r e  found efficient in destroying the protein (BRCA1) responsible for breast cancer. Keywords: Breast cancer, BRCA1 gene, pdb, BRCA1 protein   INTRODUCTION Breast cancer is the most common cancer in women worldwide. It is a type of cancer where cells in the breast divide and grow without normal control. The incidence of breast cancer has doubled during the past 30 years. Between 50 and 75 per cent of breast cancers begin in the ducts, 10 to 15 per cent begin in the lobules and a few begin in other breast tissues (Dillon et. al., 2010) According to American Cancer Society’s Global Cancer Facts and Figures, nearly 1.4 million new cases of breast cancer occurred among women worldwide in 2008. In general, developed countries have higher rates than developing countries. Although factors that make up this difference are mysterious, lifestyle and reproductive factors play a major role.  Women who carry a mutated gene of BRCA1 or BRCA2 have an increased risk of both breast and ovarian cancers. Women who have a BRCA1 or BRCA2 mutation, have a 60 to 80 per cent chance of getting breast cancer and a 15 to 60 per cent chance of getting ovarian cancer, both by the age of 70 (American Cancer Society, 2009). BRCA1 (breast cancer 1, early onset) is a human tumor suppressor gene that produces a protein called breast cancer type 1 susceptibility protein. Due to the presence of two domains viz. Zinc finger, C3HC4 type (RING finger) and BRCA1 C Terminus (BRCT) domain, the BRCA1 protein is also known as RING finger protein 53 (Paterson, 1998). The BRCA1 gene is located on 17q21 and has a total length of about 100 kb. This gene consists of 24 exons, and the coding region starts at the middle of exon (Miki et. al, 1994). The gene product of BRCA1 is a phosphorylated protein that consists of 1863 amino acids and has a molecular weight of 220kDa (Ruffner and Verma., 1997). The RING finger structure is present at the N-terminal region, and a binding site for Rad51 resides in the central part of the primary structure. Two BRCT domains, often seen in proteins that act as cell checkpoints or are involved in DNA repair, are present in the C-terminal region. The BRCT domains in BRCA1 can remodel chromatin and activate transcription (Miyake et al., 2000).  BRCA1 protein is localized in the nucleus (Wilson et al., 1999).  Recent studies have shown that small deletions, insertions, nonsense mutations and splicing aberrations account for 87% of all pathogenic mutations of the BRCA1 gene, resulting in the generation of BRCA1 protein (Couch and Weber, 1996). BRCA1 is expressed in the cells of breast and other tissues, where it helps to repair damaged DNA, or destroys cells if DNA cannot be repaired. If BRCA1 itself is damaged, damaged DNA is not repaired properly and this increases risks for cancers (Friedenson, 2007). The protein encoded by the BRCA1 gene combines with other tumor suppressors, DNA damage sensors, and signal transducers to form a large multi-subunit protein complex known as the BRCA1-associated genome surveillance complex (Wang et. al., 2000). The   Received: April 19, 2011; Revised May 19, 2011; Accepted May 19,2011.  *Corresponding Author,  Email: Senthilraja1101@gmail.com Copyright © 2011 Authors. This is an online open access articlepublished by ScholarJournals of Society for Scientific Research, and isdistributed under the Creative Commons Attribution License, whichpermits unrestricted use, distribution, and reproduction in any medium,provided the original work is properly cited. Senthil Raja et al.  10BRCA1 protein associates with RNA polymerase II, and through the C-terminal domain, also interacts with histone deacetylase complexes. Thus, this protein plays a role in transcription, DNA repair of double-stranded breaks ubiquitination (Friedenson, 2007), transcriptional regulation as well as other functions (Starita and Parvin., 2003). Women with defects in either the BRCA1 or BRCA2 gene have a greater than 80 per cent chance of developing breast cancer. The majority of breast cancer cases are due to BRCA1 and BRCA2 (Thakur and Phadke, 2005). Since, the vulnerability of BRCA1 is more than BRCA2 gene (Ford et al., 1998), in the present study only BRCA1 protein was tested against 6 chemical inhibitors derived from coastal mangrove ecosystem through bio-computational analysis.  MATERIALS AND METHODS Protein Structure The 3-D crystal structure of the targeted breast cancer protein BRCA1 (ID: 3PXB) was retrieved from the protein data bank (PDB) (www.rcsb.org/pdb). Structural and active site studies of the protein were done by using CASTP (Computed Atlas of Surface Topography of Proteins) and pymol molecular visualization software. According to Lipinski’s rule of five, a compound having not more than 5 hydrogen bond donors (OH an NH groups), not more than 10 hydrogen bond acceptors (notably N and O), molecular weight under 500 g/mol, partition coefficient log P of less than 5 and rotatable bonds of less than 10 is taken as drug molecules and docking procedure is carried out (Lipinski et al., 2001).   Chemicals screened Six chemicals namely t r i t e r p e n o i d ,  s t i g m a s t e r o l ,  r u b r o l i d e n ,  t r i c i n  a n d  N - m e t h y l f l i n d e r s i n e  identified from the coastal mangrove ecosystems (Kathiresasn and  Qasim, 2005)  were screened against the breast cancer protein (BRCA1).  Amino acid binding site The pubchem database was used for retrieving the phytochemical molecules. The selected chemical structures were generated from SMILES notation (Simplified Molecular Input Line Entry Specification) by using the Chemsketch Software (www.acdlabs.com). The predicted binding sites, based on the binding energy, and amino acids make up of the binding cavity. The predicted ligand binding site residues are listed in Table 1. Table 1.  Breast cancer protein BRCA1 binding site Amino acids in the binding pocket  Binding site amino acids in the structural unit  ALA1669, ARG1670, ARG1835 ALA1693, ALA1752, ASN1678 ALA1789, ARG1649 Alpha Helix Coil Beta strand  Docking methods  The molecular docking was performed using Argus Lab, widely distributed public domain molecular docking software. The inhibitor and target protein were geometrically optimized and docked using docking engine Argus dock. RESULTS Six chemicals derived from mangrove ecosystem were docked with protein responsible for breast cancer (BRCA1). The docked ligand molecules were selected based on docking energy and good interaction with the active site residues and the results are shown in Table 2. Of the 6 ligand molecules, 3 showed the activation energy of greater than 10 kcal/mol and the remaining 3 molecules exhibited the values less than 10 kcal/mol. The highest activation energy (- 13.0471 Kcal/mol) was found with triterpenoid (Figure 1) f o l l o w e d  b y  s t i g m a s t e r o l ,  p y r e t h r i n ,  N - m e t h y l f l i n d e r s i n  a n d  r u b r o l i d e n .  W h i l e ,  the lowest activation energy of 6.2275 Kcal/mol was found with tricin. From the in silico docking results, it is quite evident that mangrove-derived compounds have the great potential against anti tumor activity of breast cancer protein BRCA1.                 Fig 1. 3D structure of triterpenoid  Internat. Multidiscipl. Res. J. 2011, 1/1:09-12  11Table 2. Docking results of mangrove derived compounds against BRCA1 protein   Compound Name Pubchem ID Compound structure Molecular Weight [g/mol] Hydrogen  donor/ acceptor Docking Energy Level Triterpenoid CID: 9804218  458.6041[g/mol] (2,3) -13.0691 kcal/mol stigmasterol  CID: 5280794          269.082[g/mol] (1,1) -11.5995 kcal/mol pyrethrin  CID:6433155        372.454 [g/mol]   (0,5) -10.3912 k cal/mol N-Methylflindersine CID: 72819  241.2851[g/mol] C24H18N2O4 (0,2) -9.06183 k cal/mol rubrolide      CID 5472704  472.51196  (2,4) -7.8583 k cal/mol tricin CID: 5281702 CH3OOHOCH3OHOHOH330.288[g/mol] (3,7) -7.31076 k cal/mol CH3OONHOOCH3NHOOBrOHClBr OHCH 3C H 3OOOHCH 2C H 3C H 3HHHCH3CH3OHCH3CH3CH3CH3CH3CH3CH3CH3CH3CH3OHCH3O OHSenthil Raja et al.  12DISCUSSION Recent studies have shown that small deletions, insertions, nonsense mutations and splicing aberrations account for 87% of all pathogenic mutations of the BRCA1 gene, resulted in the generation of truncated BRCA1 protein (Couch and Weber, 1996).  Molecular docking is a key tool in structural molecular biology and computer-assisted drug design. Mangrove-derived compounds such as triterpenoid and stigmasterol have already been studied for computation selection against sterol carrying protein, AeSCP-2 (Senthil and Kathiresan, 2011) and cervical viral oncoprotein, HPV16 E6 (Senthil and Kathiresan, 2011). The present s tudy  a l so  proved that  the  coastal mangrove-derived compounds are capable of blocking the oncoprotein, responsible for breast cancer.  CONCLUSION Mangroves are rich in phenolic compounds of medicinal value.  These   compounds   are   ecofriendly,   safer   and cheaper fo r  appl icat ion. Identification of BRCA1 will facilitate early diagnosis of breast and ovarian cancer susceptibility in some individuals as well as a better understanding of breast cancer biology. The results obtained from this study would be useful in both understanding the inhibitory mode of mangrove- derived compounds as well as in rapidly and accurately predicting the activities of newly designed inhibitors on the basis of docking scores. Here we concluded that these compounds derived from mangrove  ecosystem (triterpenoid, s t i g m a s t e r o l  a n d  p y r e t h r i n ) could be novel chemical inhibitors for BRCA1 protein preventing the uncontrolled cell division. Further research is needed for refinement to enrich the activity of the ligands and destroying mechanism of the breast cancer protein, especially in the animal model system, and also to determine the dosage of safety levels, in order to explore this promising avenue for breast cancer control and to ensure the healthy state of women. ACKNOWLEDGEMENT We are thankful to the authorities of Annamalai University for providing necessary facilities to carry out this work. REFERENCES American Cancer Society. Breast Cancer Facts & Figures 2009-2010. American Cancer Society, 2009. American Cancer Society. Global Cancer Facts and Figures, 2nd Edition. Atlanta, GA: American Cancer Society, 2011. Couch FJ, Weber BL (1996). Mutations and polymorphisms in the familial early-onset breast cancer (BRCA1) gene. Breast Cancer Information Core. Hum Mutat 8:8–18  Dillon DA, Guidi AJ, Schnitt SJ. Chapter 28: Pathology of Invasive Breast Cancer, in Harris JR, Lippman ME, Morrow M, Osborne CK. Diseases of the Breast, 4th edition, Lippincott Williams & Wilkins, 2010. Ford D, Easton DF, Stratton M (1998). Genetic heterogeneity and penetrance analysis of the BRCA1 and BRCA2 genes in breast cancer families. The Breast Cancer Linkage Consortium. Am J Hum Genet 62:676–689) Friedenson B (2007). The BRCA1/2 pathway prevents hematologic cancers in addition to breast and ovarian cancers. BMC Cancer 7: 152.  Kathiresasn, K., S.Z. Qasim (2005). Biodiversity of mangrove ecosystems. Hindustan Publishing Corporation Limited, New Delhi, 251 pp. Senthil Raja, P and Kathiresan. K (2011). Computational selection of compounds derived from mangrove ecosystem for anti-cervical cancer activity. Journal of Recent Scientific Research Vol. 2, Issue, 4, pp. Senthil Raja, P and Kathiresan. K (2011). Computational selection of mangrove-derived compounds as mosquito larvicide’s by blocking the sterol carrying protein, AeSCP-2. Res Bioscientia, Vol. 2, Issue, 1, 1-6. Lipinski C.A., F. Lombardo, B.W. Dominy and P.J. Feeney (2001). Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv Drug Del Rev 46: 3–26. Miki Y, Swensen J, Shattuck-Eidens D, et al. (1994). A strong candidate for the breast and ovarian cancer susceptibility gene BRCA1. Science 266:66–71 Ruffner H, Verma IM (1997) BRCA1 is a cell cycle-regulate nuclear phosphoprotein. Proc Natl Acad Sci USA 94:7138–7143. Miyake T, Hu YF, Yu DS (2000). A functional comparison of BRCA1 C-terminal domains in transcription activation and chromatin remodeling. J Biol Chem 275:40169–40 173. Paterson JW (February 1998). BRCA1: a review of structure and putative functions. Dis. Markers 13 (4): 261–74. PMID 9553742. Starita, L.M.; Parvin, J.D. (2003). The multiple nuclear functions of BRCA1: transcription, ubiquitination and DNA repair. Current Opinion in Cell Biology 15 (3): 345–350. PMID 12787778. Thakur S, Phadke SR (2005). Familial breast cancer: genetics and counselling. Indian J Surg 67:297–301. Wang, Y; Cortez D, Yazdi P, Neff N, Elledge S J, Qin J (Apr. 2000). BASC, a super complex of BRCA1-associated proteins involved in the recognition and repair of aberrant DNA structures. Genes Dev. 14 (8): 927–39. PMC 316544. PMID 10783165. Wilson CA, Ramos L, Villasenor MR, et al. (1999) Localization of human BRCA1 and its loss in high-grade, non-inherited breast carcinomas. Nat Genet 21:236–240. Impact of BRCA1 BRCT domain missense substitutions on phospho-peptide recognition. (2011) Biochemistry. 

Insilico docking analysis of mangrove-derived compounds against breast cancer protein (BRCA1)

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Insilico docking analysis of mangrove-derived compounds against breast cancer protein (BRCA1)

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