Virtual Docking of VBP1 with HBX and NFκB Protein to Study the Activation of NFκB in the Regulatory Mechanism of Liver Cancer
Mamta Sagar *
Department of Bioinformatics, University Institute of Engineering & Technology and Institute of Biosciences & Biotechnology, Chhatrapati Shahu Ji Maharaj University, Kanpur, Uttar Pradesh, India.
Padma Saxena
Department of Bioinformatics, University Institute of Engineering & Technology and Institute of Biosciences & Biotechnology, Chhatrapati Shahu Ji Maharaj University, Kanpur, Uttar Pradesh, India and Department of Zoology, TRKM Aligarh, Dr BR Ambedkar University Agra, India.
Suruchi Singh
Department of Computer Science and Engineering, University Institute of Engineering & Technology, Chhatrapati Shahu Ji Maharaj University, Kanpur, Uttar Pradesh, India.
Ravindra Nath
Department of Computer Science and Engineering, University Institute of Engineering & Technology, Chhatrapati Shahu Ji Maharaj University, Kanpur, Uttar Pradesh, India.
Pramod W. Ramteke
Department of Molecular Biology & Genetic Engineering, RTM Nagpur University: Rashtrasant Tukadoji Maharaj Nagpur University, India.
*Author to whom correspondence should be addressed.
Abstract
Molecular docking is an efficient way to study protein-protein and protein-ligand interactions in virtual mode, this provides structural annotations of molecular interactions, required in the drug discovery process. The Cartesian FFT approach in ‘Hex’ spherical polar Fourier (SPF) uses rotational correlations, this method is used here to study protein-protein interactions. Hepatitis B virus (HBV) X protein (HBx) is essential for virus infection and has been used in the development of therapeutics for liver cancer. It can interact with many cellular proteins. It interferes with cell viability and stimulates HBV replication. The von Hippel-Lindau binding protein 1(VBP1) has an important role in HBx-mediated nuclear factor kappa B (NFkB) stimulation. VBP1 and HBx function as coactivators in the activation of NFκB binding. Docking results revealed that HBx and NFkB bind with VBP1 at the common site on amino acids positions Arg 161, Glu 92, and Arg 82, which may have a role in HBx-mediated NFκB activation. Lowest energy complex VBP1- NFkB1 was obtained at -883.70 Kcal/mol. The amino acids involved in interaction among HBx, VBP1, and NFκB proteins, may be involved in transcriptional regulation and has significance in normal and abnormal regulation. These amino acid interactions may be associated with the manifestation of Liver cancer.
Keywords: Hepatitis B virus (HBV) X protein (HBx), nuclear factor kappa B activity (NFkB), von hippel-lindau binding protein 1(VBP1), docking, Spherical Polar Fourier (SPF), liver cancer.