Prostate Cancer Diagnostic and Treatment Guidelines The Prostate Cancer Foundation of South Africa Publication Date: June 2013 ORIGINAL AUTHORS Prof. A M. Segone, Prof. M. Haffejee, Prof. S. Wentzel, Prof. C. F. Heyns, Prof. S. B. A. Mutambirwa, Dr. L. Coetzee, Prof. R. Barnes, D.r P. Porteous, Dr. M. Mackenzie, Dr. M.
Proceedingicgrc.ub.ac.idProceeding of 6th ICGRC 2015
6-Gingerol from Zingiberaceae as a Result of Reverse Docking
for Prostate's Cancer Potential Drug Candidate
Haqqi Anajili Setyanto1, Arindra Trisna Widiansyah1, Zainul Mustofa1 1 Postgraduate of Educational Biology, State University of Malang, Malang, Indonesia Prostate cancer is a cancer that attacks the prostate gland causing the death rate which is high enough. One of the causes ofprostate cancer is the androgen receptor (AR) in the gland cells that initiates the formation of excess cell proliferation, thuscausing prostate cancer. AR inhibitor that is known is antiandrogen (biculatamide and enzalutamide). This study aimed to test the6-gingerol compound of ginger as an AR inhibitor drug candidate for prostate cancer using silico methode. The 3D structure ofthe 6-gingerol compound was taken from PubChem, the prediction of targeted protein used SwissTargetPrediction andPharmapper, analysis and docking 6-gingerol and antiandrogens with AR using Pyrx software, visualization compounds andprotein interactions using PyMOLsoftware. Visualization results shows that the interaction of 6-gingerol, biculatamide, andenzalutamide with AR have the same site. This proves that the 6-gingerol is potential as anAR inhibitor candidate.
Keywords: 6-gingerol; prostate's cancer; reverse docking The second most common cancer diagnosed in U.S. males, after nonmelanoma skin cancer, is prostate cancer.
Estimates are that, in 2000, 180 400 cases of prostate cancer were diagnosed in the United States and 31 900 mendied of the disease . One of causing factor for prostate cancer is androgen receptor. The androgen receptor (AR)is required for prostate cancer growth in all stages, including the relapsed, androgen-independent tumors in thepresence of very low levels of androgens .The AR modulates the expression of genes involved in proliferationand differentiation. The AR belongs to the steroid receptor family of the nuclear receptor superfamily. This familyconsists of the glucocorticoid, estrogene, progesterone and mineralocorticoid receptors .
Prostate tumor cells appear to have several possible mechanisms by which they could become androgen refractory. First, mutations in the AR hormone-binding domain or amplification of the AR gene could increasetumor cell sensitivity to the very low levels of androgens that are produced by the adrenal glands. Second, mutationsof the AR could allow it to respond to other steroids or even to antiandrogens. Third, alterations of the interactionsbetween the AR and some of its coactivators could allow unmutated or mutated AR to become activated by adrenalandrogens, other steroids, or antiandrogens. Standard treatments relies on removing, or blocking the actions of,androgens.
Treatments such as androgen deprivation therapy (ADT), which typically includes suppression of testicular androgen by surgical castration or treatment with analogues of luteinizing hormone releasing hormone, are effectiveat slowing disease progression. In advanced disease, however, the cancer progresses despite low levels of circulatingandrogens that result from ADT . The novel rationally designed AR signaling inhibitor (ARSI) enzalutamide(formerly MDV3100) is a phenylthiohydantoin derivative with kla sulfonamide side chain . Enzalutamide has notonly been shown to potently inhibit the binding of androgens to the AR, but also inhibit nuclear translocation andsubsequent binding of the AR-ligand complex to DNA, thereby inhibiting transcription of AR target genes. Incontrast to antiandrogens (bicalutamide and enzalutamide) does not induce agonistic effects on AR signaling in cellsover-expressing wild type AR . 6-gingerol compounds from Zingiberaceae alleged can be used as antiandrogensfor prostate cancer treatment.
Ginger is a natural dietary ingredient with antioxidant, anti-inflammatory, and anticarcinogenic properties .
Ginger contains several pungent constituents such as gingerols, shogaols, paradols, and gingerdiols . Gingerolswere identified as the major active components in fresh ginger rhizome with 6-gingerol being the most abundantconstituent . 6-gingerol inhibited cell proliferation, induced apoptosis, and G1 cell-cycle arrest in humancolorectal cancer cells . As a drug candidate, various tests related to the degree of effectiveness are needed tothose compounds .
One of the parameters used in drug design is whether the drug candidate compound meets the Lipinski rule of five or not . Lipinski's rule of five is a rule of thumb formulated by Christopher A. Lipinski in 1997, to evaluatethe "drug-likeness" of a chemical compound, and to allow a quick, reasonably-accurate determination as to whetheror not a molecule with interesting biactive is also likely to be an orrally available drug in humans . Simply, itdefined several rules for identifying compounds with possible poor absorption and permeability . This study aimto show 6-gingerol from Zingiberaceae as drug candidate for treatment in human prostat cancer. The result of thisstudy are expected to replace antiandrogens (bicalutamide and enzalutamide) with natural product fromZingiberaceae.
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Proceeding of 6th ICGRC 2015
2. Material and Methods
2.1. Ligand preparation
Chemical 3D structure and SMILES of ligand (6-gingerol) taken from pubchem compound database  with
number ID: 442793.
2.2. Target selection Input 6-gingerol's SMILES to Pharmmapper  and SwissTargetPrediction . PharmMapper server is web server designed to identify potential target candidates for the given small molecules (drugs, natural products or othernewly discovered compounds with unidentified binding targets) using pharmacophore mapping approach .
While SwissTargetPrediction is a web server to accurately predict the targets of bioactive molecules based on acombination of 2D and 3D similarity measures with known ligands .
2.3. Molecular dockingMolecular docking 6-gingerol, target protein, and inhibitors of target protein used PyRx 0,8 software.
2.4. Visualization of molecule and small molecule interactionThe interactions 6-gingerol, target protein, and inhibitors of target protein visualyzed and analyzed using LigPlusand PyMol.
2.5. Lipinski's rule of five analysisThe drug compound tested using Molinspiration webserver to testwhether the pipelines meet the criteria ofLipinski's rule of five or not .
3. Results and Discussion
The result of target selection using Pharmmapper and SwissTargetPrediction database shows that 6-gingerol compound interact with AR in human body. The known inhibitors of androgen receptor are enzalutamide andbicalutamide. The visualization result using PyMol software shows 6-gingerol, bicalutamide and enzalutamide havethe same interaction. That interaction shows that 6-gingerol and enzalutamide interact withAR in the same site. Theinteraction of AR inhibitors is shown in Figure 2.
Figure 1. Interaction between protein target (androgen receptor) and inhibitors (6-gingerol, bicalutamide and enzalutamide) show that inhibitors bind the protein target at the same site. Information: androgen receptor (green), bicalutamide (yellow),enzalutamide (red), and 6-gingerol (blue) Protein-ligand interaction show in 2D visualization using LigPlus software. The result shows that the protein- ligand interaction between bicalutamide with AR as shown (Figure 3a) involves some amino acid residues throughhydropobic bonds, such as Glu 678, Glu 681, Pro 682, Val 685, Gly 683and with Arg 752 through both hydrophobicinteraction and hydrogen bond.On the other inhibitors, protein-ligand interaction between enzalutamide and AR(Figure 3b) also involved some amino acid residues with hydrophobic interaction, such as Pro 801, Gln 802, Phe804, Leu 805, Trp 751, Asn 756, and Thr 755. Interaction between 6-gingerol and AR as shown (Figure 3c) someamino acid residues, such as Gln 711, Trp 718, Pro 682, Leu 744, Gly 683, Lys 808, Val 715, Ala 748, Glu 681,Trp 751, Asn 756, and Thr 755. Enzalutamide and 6-gingerol have interaction with Arg 752 through bothhydrophobic interaction and hydrogen bond too.
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Proceeding of 6th ICGRC 2015
Figure 2. Visualization of Protein-Ligand interaction using Ligplus software. (a) bicalutamide with AR, (b) enzalutamide withAR, and (c) 6-gingerol withAR.
6-gingerol as drug candidate fo prostat cancer, must be test with Lipinski's rule of five. The result of the Lipinski'srule of five analysis can be seen in Table 1.
Table1. The result of the Lipinski's rule of five analysis using Molinspiration webserver AR signaling has a major role in advanced prostate cancer, which is hormone refractory or androgen independent . At this stage, even though the levels of circulating androgens are low, through variousmechanisms, such as amplification of the AR gene and upregulation of AR. The treatment for prostat cancer areusing inhibitor to block protein-ligand binding interactions of AR. The result from reverse docking of 6-gingerol andantiandrogens (bicalutamide and enzalutamide) with protein target AR, show both of inhibitors are block androgenreceptor in same site. The visualization from LigPlus shows that there are three similar amino acids which isboundto 6-gingerol and bicalutamide.Those amino acids are Glu 681, Arg 752, and Gly 683. Interactions between 6-gingerol with other antiandrogen enzalutamide also has similar amino acids bound, there are Arg 752, Trp 751, Asn756, and Thr 755.Those amino acids are actively involved in the intermolecular interaction of protein-ligandcomplex at AR.
Two or more ligands that bind on the same site of protein domain have similar biochemical mechanism and being involved in relevant biological pathway . It means that 6-gingerol has a possibility to have similarinhibitory activity with bicalutamide and enzalutamide. It shows that the 6-gingerol compound from Zingiberaceaecan be used as substitute for enzalutamide compound which has role as antiandrogens. Related to the bioavailibityand Lipinski's rule, Kujawski, et al. explained the optimal lipophilicity range along with low molar mass and lowpolar surface area is the driving force that leads to good absorption of chemicals in the intestine by passive diffusion. The rule of 5 is now implemented in our registration system for new compounds synthesized in our medicinalchemistry laboratories and the calculation program runs automatically as the chemist registers a new compound. Iftwo parameters are out of range, a poor absorption or permeability is possible alert appears on the registration screen(lipinski).According to Tabel 1, 6-gingerol have good bioavailibilty based on the lipinski's rule of five analysis. Itmeans that 6-gingerol can be used as a powerful drug candidate as a replacement of bicalutamide and enzalutamideas antiandrogens.Thus, based on this research, this compound could be the most potential drug candidate for thetreatment of prostate cancer.
6-gingerol drug candidate can be use as replacement antiandrogens (bicalutamide and enzalutamide) as prostate
Grossmann, M.E., Huang, H. Tindall, D.J. Androgen receptor signaling in androgen-refractory prostate cancer. Journal ofthe National Cancer Institute 2015; 93(22): 1687-1697.
Kaarbo, M., Klokk, T.I., Saatcioglu, F. Androgen signaling and its interactions with other signaling pathways in prostate
cancer. BioEssays 2007; 29: 1227–1238
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Waltering, K. Androgen Receptor Signaling Pathway in Prostate Cancer. University of Tampere: Academic Disertation;2010.
Dutt, S.S., and Gao, A.C. Molecular mechanisms of castration-resistant prostate cancer progression. Future Oncol 2009;
Jung, M.E., Ouk, S., Yoo, D., Sawyers, C.L., Chen, C., Tran, C., and Wongvipat, J. Structure-activity relationship for
thiohydantoin androgen receptor antagonists for castration-resistant prostate cancer (CRPC). J Med Chem 2010; 53(7):
Tran, C., Ouk, S., Clegg, N.J., Chen, Y., Watson, P.A., Arora, V., Wongvipat, J., Smith-Jones, P.M., Yoo, D., Kwon, A.,
Wasielewska, T., Welsbie, D., Chen, C.D., Higano, C.S., Beer, T.M., Hung, D.T., Scher, H.I., Jung, M.E., and Sawyers,
C.L. Development of a second-generation antiandrogen for treatment of advanced prostate cancer. Science 2009;
Baliga, M.S., Haniadka, R., Pereira, M.M,. D'Souza, J.J., Pallaty, P.L., Bhat,H.P., et al. Update on the hemopreventive
effects of ginger and itsphytochemicals. Crit Rev Food Sci Nutr 2011; 51: 499–523.
Shukla, Y. and Singh, M. Cancer preventive properties of ginger: a brief review. Food Chem Toxicol 2007; 45: 683–90.
Karna, P., Chagani, S., Gundala, S.R., Rida, P.C., Asif, G., Sharma, V., et al. Benefits of whole ginger extract in prostate
cancer. Br J Nutr 2012; 107: 473–84.
 Lee, S.H, Cekanova M, Baek SJ. Multiple mechanisms are involved in 6-gingerol-induced cell growth arrest and apoptosis in human colorectalcancer cells. Mol Carcinog 2008; 47: 197–208.
 Bean, P. New drug targets for HIV. Clinical Infectious Diseases 2005; 41: S96-S100.
 Borra, N. K. and Y. Kuna. Evolution of toxic properties of anti Alzheimer's drugs through Lipinski's rule of five. Int. J.
Pure App. Biosci. 2013; 1(4): 28-36.
 Gupta, V. Generating Three-dimensional Structure of Polymorphic Forms of CA-II Using Homology Modeling and Molecular Dynamics. ProQuest LLC., Ann Arbor.; Dissertation.
 Wheeler, R. A. and David C. Spellmeyer (Eds). Annual Reports in Computational Chemistry. Volume 5. Amsterdam; Elsevier: 2009.
 Pubchem Compound. (https://pubchem.ncbi.nlm.nih.gov/) Pharmapper. (http://184.108.40.206/pharmmapper/) SwissTargetPrediction. (http://www.swisstargetprediction.ch) Liu, Xiaofeng, Sisheng Ouyang, Biao Yu, Yabo Liu, Kai Huang, Jiayu Gong, Siyuan Zheng, Zhihua Li, Honglin Li, and Hualiang Jiang. PharmMapper server: a web server for potential drug target identification using pharmacophore
mapping approach. Nucleic Acid Research 2010; 38: W609–W614.
 Gfeller, D., A. Grosdidier, M. Wirth, A. Daina, O. Michielin and V. Zoete 2014. SwissTargetPrediction: a web server for target prediction of bioactive small molecules. Nucleic Acid Research 2014; 42: W32-8.
 Molinspiration Cheminfromatics, http://www.molinspiration.com/.) Chen, C.D., Welsbie, D.S., Tran, C., Baek, S.H., Chen, R., Vessella R., Rosenfeld MG, Sawyers CL. Molecular determinants of resistance to antiandrogen therapy. Nat Med 2004; 10: 33–39.
 Li, Q., Cheng, T., Wang, Y., and Bryant, S. Characterizing protein domain associations by small-molecule ligand binding. J Proteome Sci Comput Biol 2013; 1(6): 2050-2273
 Kujawski, J., Bernard, M.K., Janusz, A., Kuzma, W. Prediction of Log P – ALOGPS Application in Medical Chemistry Education. Journal of Chemical Education 2012; 89: 64-67.
 Lipinski, C.A., Lombardo, F., Dominy, B.W., Feeney, P.J. 1996. Experimental and Computational Approaches to EstimateSolubility and Permeability in Drug Discovery And Development Settings.Groton: Central Research Division,Pfizer Inc. CT 06340; 1996.
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FACULTY OF PHARMACEUTICAL SCIENCES JODHPUR NATIONAL UNIVERSITY Ordinance, Scheme and Syllabi for Master in Jodhpur University, Jodhpur offers Master in Pharmacy (M.Pharm.) with effect from Academic Year (2008-2009) in the following specializations:1) Pharmaceutics2) Pharmaceutical Chemistry3) Pharmacology4) Pharmacognosy5) Quality Assurance6) Clinical Pharmacy7) Industrial Pharmacy