Computational Screening of the Phytocompounds from the Plant Ballota nigra Linn against the Human Papillomavirus (HPV) E6

 

Nishandhini Marimuthu¹, Viswanathan T¹, Mahendran Radha*, Jeyabaskar Suganya

Department of Bioinformatics, School of Life Sciences, Vels University, Pallavaram, Chennai-600117,

Tamil Nadu, India.

 

ABSTRACT:

Cancer is major cause of death rate in world wide. Cervical cancer is the second most common type of cancer in women, where the cancer develops at lower part of the uterus. Literature studies clearly depicts that the mainstream of the human cervical cancers are caused by high risk HPV infections. Human Papillomavirus (HPV) E6 protein was the most prevalent high risk oncogene causing cervical cancer and still there is no proficient drug against this disease. Many researchers are involved to combat this cancer using phytodrugs.  The current research was to identify the potential plant based drug against the cervical cancer using docking studies. Docking studies of eighteen phyto compounds from the plant Ballota nigra of the family Lamiaceae were carried out using Argus Lab. From the results, Ballotinone and Ballonigrin were found to   have a best binding efficiency with the active site residues of the protein. The binding energies of the 2 compounds were -12.0691 Kcal/mol and -10.2564 Kcal/mol. This study provides promising anti-cervial cancer inhibitor for further drug development.

 

 

 

 

INTRODUCTION:

Cancer of the uterine cervix is second most common cause of female malignancies in worldwide¹. Human papilloma viruses (HPVs) of small DNA that belong to papilloma virus family, which infect mucosal epithethelial cells, genital tissues and upper respiratory tract². About, 99 % of the cervical cancer is caused by human papillomavirus³. According to the progression of malignancy, genital HPV types are divided into low-risk and high risk groups. Low-risk HPV types 6 and11 cause genital warts, which do not progress towards cancer. High risk HPV types cause malignant lesions that will promote to invasive carcinomas. High risk HPV types are seen in over 95 % of the cervical cancer⁴. Persistent HPV of high risk is found in cervical intraepithelial carcinomas⁵.

 

The HPV-16 E6 and E7 oncoproteins have ability to inactivate p53 and members of the retinoblastoma (Rb) tumour suppressor family respectively which play a major role in tumour formation. High risk viruses have been exposed to alter pathways in cell cycle and signal transduction pathways⁶.

 

HPV 16 E6 is formed by approximately 151 amino acid protein with two zinc finger joined by an interdomain linker of 36 amino acid, flanked by short amino (N) and carboxyl(C) terminal domains⁷. Inactivation of Mdm2 pathway, occurs when E6 protein arrest the proapoptoptic activity of p53 by interacting with a plethora of cellular proteins⁸. Ubiquitin mediated degradation occurs when E6 binds to p53 in the cytoplasm by blocking its translocation to the nucleus. Thus by preventing the p53 translocation will repress the tumour growth⁹.

 

Effective treatment against the HPV infection is still unavailable. So there is an urgent need for the promising drug against cancer. For many decades, Plant has been an important source of herbal medicine, because of the presence of various health’s sustaining constituents. The foremost objective of this research study is to identify the bioactive compound from the natural plants that produce physiological actions on the human body.

 

Ballota nigra (Black horehound) is a perennial herb of the family Lamiaceae. The plant is used to treat nervous disorders, stomach cramps, whooping cough, diabetes and gastrointestinal disorders^10-12. Therefore, the present study was made to screen the eighteen compounds from the plant and their interaction with the active site residues of the protein HPV16 E6 using docking studies.

 

MATERIALS AND METHODS:

Computational Methodology:

Protein Preparation and energy minimization:

The three dimensional structure for Human Papilloma virus E6 oncoprotein (1VZN) was retrieved from Protein Data Bank. Then the protein chosen for the study should be optimized by removing water molecules, ions, ligands from the structure file. Further, the hydrogen atoms present in the protein are optimized and minimized according to Hartree-Fock calculation method of Argus lab.

 

Preparation of Ligand structures:

The natural compounds used for the docking study were selected from the literature studies. Eighteen phyto compounds from the plant Ballota nigra were chosen for the study. These structures were retrieved from Pubchem and some of the ligand structures were drawn using chemsketch. Further, optimization of the compound structure was carried out using Hartree–Fock (HF) calculation method using ArgusLab.

 

Active site Prediction:

Identification of active site is often the initial point in protein–ligand binding site prediction for structure-based drug design.  Active site of the protein was obtained using the metapocket. Metapocket uses interaction energy and a simple Vander Waals probe to locate energetically favorable binding sites of the protein. The most potential binding site of the protein was analysed.

 

Molecular Docking Study:

Molecular Docking of the protein and ligands were performed using Argus Lab 4.0.1. Docking was performed using “Argus Dock” with exhaustive search docking function of ArgusLab with a grid resolution of 0.40 Å. Protein structure of HPV 16 E6 (1vzn) was loaded and the binding site of the protein were analyzed. Then the compounds chosen for the study were introduced and the docking analysis were performed by shape based algorithm and the flexible docking of the ligands by Ascore scoring function.  Docking of the protein- ligand complex was evaluated by scoring function. 10 independent runs were conducted and one pose for each complex structure was obtained. The stability of the docking complex was analyzed by lowest Ascore and hydrogen bond interactions.

 

RESULTS AND DISCUSSION:

Natural inhibitors from the plant were docked with active site residues of the protein HPV 16 E6. The active site residues obtained from metapocket were listed in the Table1.Among the eighteen compounds, Ballotinone and Ballonigrin showed a lowest binding energy of -12.0691 Kcal/mol and -10.2564 Kcal/mol. Ballotinone was found to interact with  E6 residues of Leu 45 and Glu 120 by forming hydrogen bonds, Where as the compound Ballonigrin was found to interact with the residue of Tyr 83 by forming hydrogen bond are shown in the Figure 1.Of all compounds, five compounds showed least binding energy and their interactions with the residue, hydrogen bond distance  are given in the Table 2.

 

Table 1: Catalytic site residues of HPV 16 E6 protein

Amino acid residue in the active site	Structural unit of the residues
Gln13,Cys 37,Val 38,Cys 40,Lys 41gln 42,Leu 44,Leu 45,Glu 48,Val 49, Asp 51,Phe 52,Arg 55,Ser 78,Lys 79,Ser 81,Glu 82,Tyr 83,His 85,Tyr 86,Ser 89, Arg 109,Cys 110, Pro 116,Leu 117,Cys 118,Pro 119,Glu 120,Lys 122 and Leu 126	Helix
Leu 19, Pro 20, Gln 21, Leu 22,cys 23,Thr 24, Leu 26, Lys101Cys 113, Gln 114and Lys 115	Coil
Gln 97, Gln 98, Tyr 99, Asn 100, Leu 103and Asp 105	sheet

 

a. Ballotinone with HPV 16 E6

 

b. Ballonigrin with HPV 16 E6

 

Figure 1: Docking of HPV 16 E6 protein with Ballotinone and Ballonigrin

 

 

Table 2: Interactions of HPV 16 E6 protein with compounds from Ballota nigra

 

Our docking result revealed, the compounds from the plant were known to inhibit he protein HPV 16 E6 of cervical cancer. Interaction of the compounds with amino acid residues of p53 binding, which prevent E6 protein from binding with p53 protein. 

 

CONCLUSION:

The molecular interaction between the HPV 16 E 6 protein and p53 show a major crucial role in cervical cancer. Hence, molecular docking studies of the compounds against the active site of the protein HPV 16 E6. From the results, it is revealed that Ballotinone and Ballonigrin showed high binding affinity towards the protein by disrupting the human tumor suppressor protein p53-HPV oncoprotein complex. In conclusion, few compounds of the plant Ballota nigra could be the successful drug against cervical cancer. This study is further investigated in drug designing for development of effective therapeutic medicine against cervical carcinoma.

 

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Accepted on 12.06.2017        © RJPT All right reserved

Research J. Pharm. and Tech 2017; 10(9):3095-3097.