RESEARCH ARTICLE


Bioinformatics Based Understanding of Effect of Mutations in the Human β Tubulin Outside Drug Binding Sites and its Significance in Drug Resistance



Selvaa Kumar C1, *, Debjani Dasgupta1, Nikhil Gadewal2
1 School of Biotechnology and Bioinformatics, DY Patil University, CBD Belapur, Navi Mumbai 400614, India
2 Advanced Centre for Treatment, Research and Education in Cancer, Kharghar, Navi Mumbai 410210, India


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© 2018 Kumar C et al.

open-access license: This is an open access article distributed under the terms of the Creative Commons Attribution 4.0 International Public License (CC-BY 4.0), a copy of which is available at: (https://creativecommons.org/licenses/by/4.0/legalcode). This license permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

* Address correspondence to this author at the School of Biotechnology and Bioinformatics, DY Patil University, Selvaa Kumar C, CBD Belapur, Navi Mumbai 400614, India; Tel: 912227563600; Email: selvaakumarc@gmail.com


Abstract

Background:

Human β tubulin displays resistance to drugs like Taxol and Vinblastine due to amino acids substitutions within and outside the drug binding site.

Objective:

This study focuses on the effect of amino acid substitutions outside the drug binding site on drug resistance. Amino acid substitution like R306C (mut2) is associated with Taxol resistance and D197N (mut1) and K350N (mut3) are associated with Vinblastine resistance. However, the mechanism of resistance has not been understood yet. This study has attempted to investigate the mechanism of resistance.

Methods:

SWISSMODEL server was used to model the wild and the mutant β subunits which were later considered for protein-protein and protein-ligand docking using HADDOCK and AutoDock 1.5.6 software respectively. Dimer mutants were generated using Swisspdbviewer. POCASA 1.1 server was used to calculate the overall effect of substitution on pocket volume and the effect of substitution on domain mobility was explored using GROMACS software.

Results:

From sequence perspective, amino acid replacement in all three positions viz. D197N (mut1), R306C (mut2) and K350N (mut3) were found to have a deleterious effect on the stability of the protein. This study was further confirmed through structural analysis. Change in hydrogen bonding pattern was observed within the site of substitution in modeled mut1 and mut3 which is known to be specifically involved in Vinblastine interaction. In mut2 associated with Taxol binding, the hydrogen bonding pattern remained unaltered. All three mutants showed better protein-protein (β-β) interactions compared to the wild-type. Pocket size analysis in β subunit revealed that Taxol binding site increased in size after substitution in mut2 compared to the wild-type. However, the size of the Vinblastine binding site in the dimer interface remained the same before and after the substitution in wild and the mutants. Wild-type (β monomer and αβ dimer) associated with Taxol and Vinblastine, respectively showed better drug interaction compared to their mutants.

Conclusion:

This study throws light on the mechanism of drug resistance due to amino acid substitutions outside the drug binding site. It was found that amino acid substitution outside the drug site enhanced protein-protein interaction between the β-β subunits.

Keywords: R306C, D197N, Drug resistance, K350N, Taxol, Tubulin mutations, Vinblastine.