Int. J. Mol. Sci. 2015, 16, 2747-2766; doi:10.3390/ijms16022747
International Journal of
ISSN 1422-0067 www.mdpi.com/journal/ijms
Binding Mode Analysis of Zerumbone to Key Signal Proteins in the Tumor Necrosis Factor Pathway
Ayesha Fatima1,2,*, Ahmad Bustamam Hj. Abdul 1, Rasedee Abdullah 1,3,
Roghayeh Abedi Karjiban 4,5 and Vannajan Sanghiran Lee 6,* 1 UPM-MAKNA Cancer Research Laboratory, Institute of Biosciences, University Putra Malaysia, 43400 Serdang, Malaysia; E-Mails: firstname.lastname@example.org (A.B.H.A.); email@example.com (R.A.) 2 Faculty of Pharmaceutical Sciences, UCSI University, 1-Jalan Menara Gading, Taman Connaught,
Cheras, 56000 Kuala Lumpur, Malaysia 3 Department of Microbiology and Pathology, Faculty of Veterinary Medicine,
University Putra Malaysia, 43400 Serdang, Malaysia 4 Department of Chemistry, Faculty of Science, University Putra Malaysia, 43400 Serdang, Malaysia;
E-Mail: firstname.lastname@example.org 5 Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and
Biomolecular Sciences, Universiti Putra Malaysia, 43400 Selangor, Malaysia 6 Department of Chemistry, Faculty of Science, University Malaya, Petaling Jaya, 50603 Selangor, Malaysia * Authors to whom correspondence should be addressed;
E-Mails: email@example.com (A.F.); firstname.lastname@example.org (V.S.L.);
Tel.: +603-7967-7022 (ext. 2142) (V.S.L.); Fax: +603-7967-4193 (V.S.L.).
Academic Editor: Christo Christov
Received: 24 October 2014 / Accepted: 7 January 2015 / Published: 26 January 2015
Abstract: Breast cancer is the second most common cancer among women worldwide.
Several signaling pathways have been implicated as causative and progression agents. The tumor necrosis factor (TNF) α protein plays a dual role in promoting and inhibiting cancer depending largely on the pathway initiated by the binding of the protein to its receptor.
Zerumbone, an active constituent of Zingiber zerumbet, Smith, is known to act on the tumor necrosis factor pathway upregulating tumour necrosis factor related apoptosis inducing ligand (TRAIL) death receptors and inducing apoptosis in cancer cells.
Zerumbone is a sesquiterpene that is able to penetrate into the hydrophobic pockets of
Int. J. Mol. Sci. 2015, 16 2748 proteins to exert its inhibiting activity with several proteins. We found a good binding with the tumor necrosis factor, kinase κB (IKKβ) and the Nuclear factor κB (NF-κB) component proteins along the TNF pathway. Our results suggest that zerumbone can exert its apoptotic activities by inhibiting the cytoplasmic proteins. It inhibits the IKKβ kinase that activates the NF-κB and also binds to the NF-κB complex in the TNF pathway. Blocking both proteins can lead to inhibition of cell proliferating proteins to be downregulated and possibly ultimate induction of apoptosis.
Keywords: zerumbone; Inhibitor of κ-B kinase (IKK); nuclear factor κ-light-chain-enhancer of activated B cells (NF-κB); CHARMm based docking software (CDOCKER); molecular docking 1. Introduction
Cancer is one of the leading causes of deaths worldwide . In Malaysia, lung cancer (16.3%) and breast cancer (32.1%) account for the leading causes of death among males and females, respectively .
Several available options of anticancer drugs are non-selective and toxic. This evident void generates the need for finding newer and safer therapies. The use of alternate medicine has always been an interesting area in medical explorations. Several studies have reviewed the use of herbal drugs alone and in combination with chemotherapy to inhibit the progression of the disease [3–9].
Zerumbone is a sesquiterpene obtained from Zingiber zerumbet Smith. It is known to exhibit anti-cancer activity against several cancers by modulating several proteins to induce apoptosis .
Several articles have identified key proteins that can be inhibited by zerumbone for arresting cancer cell growth [11–19]. Prasannan et al.  reviewed key pathways such as tumor necrosis factor signaling pathway and the phosphinositide-3-kinase/Akt/mTOR pathway modulated by zerumbone.
It has shown anti-inflammatory and chemopreventive activity against colon and skin cancer [14,20,21].
Reports have also been published on the apoptotic activity of zerumbone on liver, ovary and cervix as well as leukemia [11–13,16,18]. It has been reported to act as a modulator of osteoclastogenesis induced by receptor activated NF-κB ligand (RANKL) and breast cancer . Figure 1 shows the effect of zerumbone on the TNF pathway and RANKL.
Although zerumbone has been studied extensively in the laboratory, but determining the precise binding target and the molecular level events that may occur between the drug and target has not fully understood. Some researchers have reported that the apoptotic mechanism of zerumbone could be due to the formation of Michael adducts that it is an unsaturated carbonyl group forms with glutathione to remove it, which increases the intracellular redox potential of cancerous cell as compared to the normal cells, ultimately leading to apoptosis of the cancer cells [11,23]. Ligand protein interactions can be investigated using docking programs. Docking techniques are useful since they allow a better understanding of the molecular events happening at the binding interface of ligand-protein interaction site. Their utility is paramount in complementing and supplementing the experimentally determined data. Using CHARMm based docking software (CDOCKER) of the Discovery Studio 2.5.5 (Accelrys
Inc., San Diego, CA, USA) suite of programs, docking studies were carried out to evaluate which
Int. J. Mol. Sci. 2015, 16 2749 proteins are the most likely targets of zerumbone and determine the exact binding mechanism of the molecule with its target protein [24,25]. CDOCKER applies grid-based molecular dynamics simulated annealing protocol by using CHARMM force field while devising the appropriate position of the ligand in the active pocket. The algorithm offers flexible ligand docking where the non-bonded interactions are softened during the docking procedure but removed during the final minimization process . The protein was held rigid during the entire process.