Albany 2019: 20th Conversation - Abstracts

category image Albany 2019
Conversation 20
June 11-15 2019
Adenine Press (2019)

Tongue tumour protein BAH14511.1 Sequence analysis and homology modelling to find out interacting binder network through molecular docking

Day by day, people are dying of one or the other type of cancer worldwide; oral cancer being the third most common cancer in India and sixth in the world. To treat cancer, the roles of different factors involved in triggering cancer needs to be exploited which needs the exploration of mechanisms of the factors involved and targeting their interactions with co-operating factors (Takiar et al., 2010; van der Wall, 2013). The protein product with accession number BAH14511.1, isolated from tongue tumour tissue of Homo sapiens was found to be an isoform b of cGMP dependent protein kinase II (PKGII) as shown by the results of non-redundant BLAST. PKGII plays an important role in the regulation of signalling pathways associated with cancer, and hence prediction of the 3D structure of the isoform would be important for the prediction of lead molecules that can be further used for designing a drug for the regulation of PKGIIb. In this study, various tools (PROTPARAM, SMART, TMHMM, SignalP, SecretomeP, NetChop and NetPhos) were used for functional annotation. The 3D structure of the protein was predicted by Homology Modelling approach (Blom et al, 1999; YU et al., 2006). The 3D structure was validated by Verify3D and WhatIf. The binding site in the 3D structure of PKGIIb was predicted by using SiteMap which gave 5 sites as result from which the site having highest site score of 1.114 and volume 348.145 was further used for docking and virtual screening. The predicted 3D structure was used to screen the NCI database for finding potential binders. The structures from the NCI database were docked with the 3D structure of the protein and the best docking score of -12.547 was obtained. All the compounds binding with the protein followed Lipinski’s Rule. The top structures from the NCI database have been reported as potential binders of the protein. The binding affinity of the top binder NSC1972 was found to be -63.296 as predicted by PRIME MM-GBSA and Induced-fit docking was done to validate docking results.


    Takiar R, Nadayil D and Nandakumar A (2010) Projections of number of cancer cases in India (2010-2020) by cancer groups. Asian Pac J Cancer Prev. 11(4) :1045-9.

    van der Waal I (2013) Are we able to reduce the mortality and morbidity of oral cancer; Some considerations. Med Oral Patol Oral Cir Bucal. 18(1) :e33-7.

    Blom N, Gammeltoft S and Brunak S (1999) Sequence- and structure-based prediction of eukaryotic protein phosphorylation sites. Journal of Molecular Biology 294(5) :1351-1362.

    Yu CS, Chen YC, Lu CH and Hwang JK (2006) Prediction of protein subcellular localization. Proteins: Structure, Function and Bioinformatics 64 :643-651.

Snigdha Singh and
Ramesh Chandra

Drug Discovery & Development Laboratory
Department of Chemistry
University of Delhi
Delhi-110007, India.

E-mail: acbrdu@hotmail.com