Exploring structural properties of alginate derivatives based on QM/MM approach
Volume Title: 1
1Department of Biotechnology, Karunya Institute of Technology and Sciences, Karunya Nagar,Coimbatore-641114, Tamil Nadu, India
2Biomedical Engineering Department, Faculty of Chemical Engineering, Tarbiat Modares University, Tehran, Iran
Alginate is a linear acidic polysaccharide which has three types of block arrangement: polymannuronate (polyM), polyguluronate (polyG), and the combination of both groups. In this study, quantitative structure property relationship (QSPR) of alginate derivative was investigated and 3D structure of 158 alginate molecules were optimized. Among 158 alginate compounds, one compound of alginate was identified as the compound that could satisfy the Lipinski’s rule of five totally.The absorption, distribution, metabolism, elimination and toxicity (ADMET) properties of alginate derivatives for the druggability was predicted and only one compound was identified as the compound that could satisfy Lipinski’s rules of five. With the help of molecular mechanics, binding energy was determined as -7.75 kcal/mol and the interaction of alginate derivatives with alginate binding protein was investigated. These information can be utilized to design most potent therapeutic affinity, selectivity with competent target of alginate binding protein based on structural similarity search approach.
alginate derivative; quantitative structure property relationship; alginate-binding protein; druggability