Silico docking studies of phytocompounds biology essay

Bioinformatics Centre (DIC), Kerala Agricultural University, Vellanikkara, Thrissur 680 656, Kerala.


Lekshmysree S Nair : lekshmy. [email protected] comMekha Mohan : [email protected] comR. Keshavachandran : [email protected] comP. A. Nazeem : [email protected] com



Cancer cell invasion and metastasis are multistep processes influenced by the over expression of cell-secreted proteolytic enzymes such as Matrix metalloproteinases (MMPs). Strategies to down regulate MMP expression could be a breakthrough in cancer therapy. Phosphatidylinositol 3-Kinase/NF-κB signaling pathways have been known to be involved in regulating MMP-9 expression. Synergistic targeting of these pathways using NF-kB and PI3-kinase inhibitors may have a therapeutic potential for the treatment of cancer. Plants have been elucidated as therapeutic source for curing diseases. One of the most feasible approaches for cancer treatment is by untapping the therapeutical value of phytochemicals . This paper focuses on identifying phytocompounds having anti-cancer potential to effectively inhibit PI3K and NF-kB . Results: We selected thirty five phytocompounds with anticancer properties. Five compounds namely allixin, capsaicin, eugenol, niazimicin and piperine were screened using Lipinski rule of five and ADMET. These five compounds were docked with PI3K and NF-kB proteins. All the five ligands showed interaction with the two proteins and the residues showed maximum interaction for Pi3K and NF-kB respectively. Niazimicin exhibited maximum interaction for both PI3K and NF-kB. Conclusion: We demonstrated that in silico docking experiment can be effectively carried out to identify phytocompounds that effectively inhibit the target proteins. Interestingly we found that niazimicin, a phytocompound of Moringa Oleiferaw which is not yet completely exploited for their medicinal properties showed maximum interaction with the target proteins. We also identified that Cys37 of the enzyme plays an important role in hydrogen bonding with inhibitors. This residue can be considered to being an active site for anti-cancer drug design. Keywords: Cancer Metastasis Phosphoinositide 3-kinase MMP-9 Nuclear factor of kappaB Niazimicin moringa oleifera


Cancer is a potentially fatal disease characterized by uncontrolled cell growth. Most of the emphasis in cancer research had been on the pathogenesis of primary tumors. But now, the major concern while diagnosing cancer is whether or not the cancer has already metastasized. Metastatic disease is usually a signal of immediate patient death. Understanding the complex pathways involved in cancer cell invasion and metastasis is a promising step towards identifying molecular targets for cancer therapy. Metastasis involves the progression of tumor in situ to an invasive tumor. It consists of a cascade of linked, sequential steps by which a subset or individual cancer cells disseminate from a primary location to distant secondary organs or tissues. Invasion involves tumor cell adherence to cells and to the extracellular matrix (ECM), proteolytic degradation of the surrounding tissue and acquisition of tumor cell motility [1]. The secretion of extracellular proteases plays an important role in cancer cell metastasis [2]. Of these proteases, the matrix metalloproteinases (MMPs), a group of zinc-dependent ECM-degrading enzymes play a pivotal role in tumor invasion, migration, host immune escape, extravasation, angiogenesis, and tumor growth. MMPs especially MMP-9 have increased expression for various types of tumor progression [3]. The elevation in MMP-9 production was mediated by the enhanced activity of PI3K [4]. PI3K is highly mentioned for its involvement in the developmental stages of tumor. The PI3K family constitutes a large family of lipid and serine/threonine kinases divided into different classes. They are composed of regulatory and catalytic sub unit. The oncogenic transformation has been reported to be induced by the over expression of different isoforms of the various subunits such as the catalytic subunit, p110. This is contributed by the mutation in the genes encoding these subunits [5-7]. PI3K regulate motility of invasive cancer cells by the activation of transcription factor, NF-kB [8-10]. Nuclear factor of kappaB (NF-kappaB) is a sequence-specific transcription factor involved in inflammatory and innate immune responses. . Although this factor is expressed in an inactive state in most cells, cancer cells express an activated form of NF-kB. PI3k regulated downstream cellular events include inactivation of several proapoptotic factors like BAD, procaspase-9, Forkhead (FKHR) transcription factors etc and the activation of transcription factors that upregulate antiapoptotic genes, including NF-κB [11-14]. MMP-9 has a nuclear factor-kB (NF-kB) binding site in its promoter region which is activated through the PI3-k pathway [15][16]. The expression of tumor MMP-9 is therefore in an NF-kB dependent manner and is correlated with PI3k pathway [17]. Inhibition of the PI3K pathway components could synergize with, or overcome resistance to the existing cancer therapies [18]. Inhibitors could either target all isoforms of a particular protein or specifically a particular isoform. A drug targeting an upstream pathway component is unlikely to respond to downstream-activated mutation. Therefore inhibitors targeting both upstream and downstream components could be a breakthrough in cancer therapy. Plant kingdom represents an excellent reservoir of organic compounds, many of which have been used for medicinal purposes. Phytocompounds could serve as lead for developing novel agents having good efficacy in various diseases. Exploration of these phytochemical constituents and their pharmacological screening will thus provide basis for developing new life saving anti cancer drugs.


Protein selection and preparation of protein data bank file

Crystal structures of Phosphoinositide-3-kinases/PI3K(1E8Y) with resolution 2. 00A° and NF-kB/p50 (1NFK) with resolution 2. 3A° were downloaded from protein data bank (PDB) (www. rcsb. org) . The protein structures were subjected to preparation prior to minimization. Crystallographic water molecules and ligands were removed from the protein. Chemistry of the proteins were corrected by adding hydrogen. Energy minimization was performed using CHARMm force field to relax the confirmation and to remove steric overlap.

Ligand preparation

About 35 phytocompounds with anticancer properties were selected for the study. The three dimensional structure of these phytocompounds was downloaded in . sdf format from Pubchem database (www. ncbi. nlm. nih. gov/pubchem). Lipinski’s properties like molecular weight, log P and number of Hydrogen-bond donors and acceptors for the active phytocompounds were calculated and ligands were screened on the basis of these properties. The ADMET properties for the phytocompounds which satisfies the Lipinski properties were calculated by using the toxicity prediction protocol of Discovery studio (ADMET). The ADMET properties include Aqueous solubility, Blood-brain penetration level, Cytochrome 450 (CYP450), Hepatotoxicity, Human Intestinal Absorbtion and Plasma protein binding level.


The binding sites of both proteins were predicted using receptor-ligand interaction protocol. For each binding site, the ligands were docked to get the poses of interaction. Ligand fit protocol was used for performing docking. The ligand binding affinity was calculated using LigScore, PLP1 and PLP2. JAIN and Dock score were used to estimate the ligand-binding energies. All the other input parameters were set as default options.

Toxicity prediction

Ligands with clogP lesser than 5, logS greater than -4, molecular weight lesser than 450, positive value for drug likeness and maximum drug score, possess qualities of less toxic traded drugs. Toxicity risk assessment and drug properties are displayed with green indicating low risk, yellow indicating medium risk and red indicating high risk.

Result and Discussion

Binding site prediction

The active sites were predicted for the energy minimized structures of 1E8Y and 1NFK with receptor – ligand protocol of discoverystudio. 37 and 17 sites were predicted for 1E8Y and 1NFK respectively.

Ligand selection

Molecular weight, logp, number of hydrogen bond donors and acceptors for the active phytocompounds according to Lipinski rule of five [22][23] are tabulated in Table-1. Twenty one ligands out of thirtyfive satisfied Lipinski’s rule of five. The compounds for docking with Pi3K and NF-kB were chosen based on its toxicity. Table-2 shows the ADMET (Absorbtion, Distribution, Excretion, Metabolism, Toxicology) properties of the compounds which already satisfied the Lipinski properties. Many compounds even after getting approval fail to reach market due to its toxicity [24]. After screening the 21 phytocompounds, five compounds namely allixin, eugenol, capsaicin, peperine and niazimicin were selected for docking studies.

Docking of Pi3k (1E8Y) and NF-kB (1NFK) with the five ligands

Docking of Pi3k and NF-kB were performed with the selected ligands. The final docked conformations obtained for the different ligands were evaluated based on the docking score and the number of hydrogen bonds formed, as given in Table 3, Table 4 and Figure 1. Docking score is a measure of interaction of ligand to the active site of the target. Greater values of dockscore and more number of H-bonds formed between the atoms in the active site of the targets and ligands indicate effective stable conformation of the bound target-ligand.

Toxicity prediction

Toxicity analysis was performed for all the five ligands by OSIRIS property explorer. Ligands were drawn availing the drawing options of OSIRIS. The various molecular properties such as clogP, Solubility, Molecular weight, drug likeness and drug score were calculated and displayed as given in Table 5 and figure 2. Toxicity risk assessment was interpreted as green indicating – low risk, yellow indicating -medium risk, red indicating – high risk.


Among the five ligands, Niazimicin which is an active compound of Moringa Oleifera showed maximum interaction for both Pi3k and NF-kB with dockscore values 60. 314 and 48. 098 respectively. Niazimicin satisfied all the qualities of a less toxic drug except a negative value of -0. 88 for drug likeness. But it gave a better drug score of 0. 57. Also, the other factors such as mutagenicity, tumorigenicity, irritating effects and reproductive effects fall within the desirable limits as indicated by the green marking. It can therefore be categorized in the medium to low risk group. The therapeutic value of niazimicin can be effectively used to inhibit Pi3k mediated NF-kB pathway. This study is an insilico approach to reiterate the application of these anti-cancer phytochemicals of Moringa oleifera as the potent and safe natural therapeutic agents in cancer drug design. With increasing evidences supporting the molecular mechanism underlying the anticancer potential of Moringa coupled with considerations of quality, safety, and efficacy could be a breakthrough in developing new anticancer drugs and adjuvants to current therapy.


The financial support extended by the BTIS (Biotechnology information system), DBT (Department of Biotechnology), Ministry of Science and Technology, Government ofIndia, India is acknowledged.